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"Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-CoV-2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": 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"https://www.iedb.org/epitope/1310502", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1330542", "url": "https://www.iedb.org/epitope/1330542", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1334359", "url": "https://www.iedb.org/epitope/1334359", "database": "IEDB", "categories": [ "Other" ] }, { "id": "2134048", "url": "https://www.iedb.org/epitope/2134048", "database": "IEDB", "categories": [ "Other" ] }, { "id": "IPR044342", "url": "https://www.ebi.ac.uk/interpro/entry/IPR044342", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "pdb_00007yc2", "url": "https://www.rcsb.org/structure/pdb_00007yc2", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7YC2", "url": "https://www.rcsb.org/structure/7YC2", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "PF27997", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF27997", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "YP_009725255", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009725255", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "A0A663DJA2-1", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2-1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "sequence": { "sequence": "MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT", "length": 38, "header": "sp|A0A663DJA2-1|ORF10_SARS2 Isoform 1 of Putative ORF10 protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=ORF10 PE=5 SV=1 CANONICAL=A0A663DJA2-1" }, "isoforms": [ { "isoform_ac": "A0A663DJA2-1", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2/entry#A0A663DJA2-1", "sequence": { "sequence": "MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT", "length": 38, "header": "sp|A0A663DJA2-1|ORF10_SARS2 Isoform 1 of Putative ORF10 protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=ORF10 PE=5 SV=1 CANONICAL=A0A663DJA2-1" }, "locus": {} } ], "glycosylation": [], "phosphorylation": [], "glycation": [], "keywords": [], "publication": [ { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States.", "journal": "Emerg. Infect. Dis.", "date": "2020", "authors": "Harcourt Jennifer, Tamin Azaibi, Lu Xiaoyan, Kamili Shifaq, Sakthivel Senthil K, Murray Janna, Queen Krista, Tao Ying, Paden Clinton R, Zhang Jing, Li Yan, Uehara Anna, Wang Haibin, Goldsmith Cynthia, Bullock Hannah A, Wang Lijuan, Whitaker Brett, Lynch Brian, Gautam Rashi, Schindewolf Craig, Lokugamage Kumari G, Scharton Dionna, Plante Jessica A, Mirchandani Divya, Widen Steven G, Narayanan Krishna, Makino Shinji, Ksiazek Thomas G, Plante Kenneth S, Weaver Scott C, Lindstrom Stephen, Tong Suxiang, Menachery Vineet D, Thornburg Natalie J", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32160149", "url": "https://glygen.org/publication/PubMed/32160149" } ] }, { "title": "Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy.", "journal": "Clin. Microbiol. Infect.", "date": "2020", "authors": "Capobianchi M R, Rueca M, Messina F, Giombini E, Carletti F, Colavita F, Castilletti C, Lalle E, Bordi L, Vairo F, Nicastri E, Ippolito G, Gruber C E M, Bartolini B", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32229288", "url": "https://glygen.org/publication/PubMed/32229288" } ] }, { "title": "Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2.", "journal": "Emerg. Infect. Dis.", "date": "2020", "authors": "Lau Susanna K P, Luk Hayes K H, Wong Antonio C P, Li Kenneth S M, Zhu Longchao, He Zirong, Fung Joshua, Chan Tony T Y, Fung Kitty S C, Woo Patrick C Y", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32315281", "url": "https://glygen.org/publication/PubMed/32315281" } ] }, { "title": "Isolation of infectious SARS-CoV-2 from urine of a COVID-19 patient.", "journal": "Emerg. Microbes Infect.", "date": "2020", "authors": "Sun Jing, Zhu Airu, Li Heying, Zheng Kui, Zhuang Zhen, Chen Zhao, Shi Yongxia, Zhang Zhaoyong, Chen Si-Bei, Liu Xuesong, Dai Jun, Li Xiaobo, Huang Shuxiang, Huang Xiaofang, Luo Ling, Wen Liyan, Zhuo Jianfen, Li Yuming, Wang Yanqun, Zhang Lu, Zhang Yanjun, Li Fang, Feng Liqiang, Chen Xinwen, Zhong Nanshan, Yang Zifeng, Huang Jicheng, Zhao Jincun, Li Yi-Min", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32342724", "url": "https://glygen.org/publication/PubMed/32342724" } ] }, { "title": "An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020).", "journal": "J. 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Commun.", "date": "2020", "authors": "Shannon Ashleigh, Selisko Barbara, Le Nhung-Thi-Tuyet, Huchting Johanna, Touret Franck, Piorkowski G\u00e9raldine, Fattorini V\u00e9ronique, Ferron Fran\u00e7ois, Decroly Etienne, Meier Chris, Coutard Bruno, Peersen Olve, Canard Bruno", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32943628", "url": "https://glygen.org/publication/PubMed/32943628" } ] }, { "title": "Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients.", "journal": "Int. J. Infect. Dis.", "date": "2020", "authors": "Lednicky John A, Lauzard Michael, Fan Z Hugh, Jutla Antarpreet, Tilly Trevor B, Gangwar Mayank, Usmani Moiz, Shankar Sripriya Nannu, Mohamed Karim, Eiguren-Fernandez Arantza, Stephenson Caroline J, Alam Md Mahbubul, Elbadry Maha A, Loeb Julia C, Subramaniam Kuttichantran, Waltzek Thomas B, Cherabuddi Kartikeya, Morris J Glenn, Wu Chang-Yu", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "32949774", "url": "https://glygen.org/publication/PubMed/32949774" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser 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Microbes Infect.", "date": "2021", "authors": "Neira V\u00edctor, Brito B\u00e1rbara, Ag\u00fcero Bel\u00e9n, Berrios Felipe, Vald\u00e9s Valentina, Gutierrez Alberto, Ariyama Naomi, Espinoza Patricio, Retamal Patricio, Holmes Edward C, Gonzalez-Reiche Ana S, Khan Zenab, van de Guchte Adriana, Dutta Jayeeta, Miorin Lisa, Kehrer Thomas, Galarce Nicol\u00e1s, Almonacid Leonardo I, Levican Jorge, van Bakel Harm, Garc\u00eda-Sastre Adolfo, Medina Rafael A", "evidence": [ { "database": "UniProtKB", "id": "A0A663DJA2", "url": "https://www.uniprot.org/uniprotkb/A0A663DJA2" } ], "reference": [ { "type": "PubMed", "id": "33317424", "url": "https://glygen.org/publication/PubMed/33317424" } ] }, { "title": "Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China.", "journal": "Emerg. Infect. 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0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 41 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "uniprot_canonical_ac": "P0DTC1-1", "uniprot_ac": "P0DTC1", "uniprot_id": "R1A_SARS2", "mass": { "chemical_mass": 489989.0, "monoisotopic_mass": 489989.0 }, "refseq": { "ac": "YP_009725295", "name": "ORF1a polyprotein", "summary": "", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009725295" }, "gene_names": [], "protein_names": [ { "name": "Replicase polyprotein 1a", "type": "recommended", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "2.7.7.50", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "GFL", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Growth factor-like peptide", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Leader protein", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Main protease", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Mpro", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 1", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 3", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 5", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 9", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "ORF1a polyprotein", "type": "synonym", "evidence": [ { "id": "YP_009725295", "database": "RefSeq", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009725295" }, { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "PL-PRO", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "PL2-PRO", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "Papain-like proteinase", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "SARS coronavirus main proteinase", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "nsp1", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "nsp3", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "nsp5", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "nsp9", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "p65 homolog", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] }, { "name": "pp1a", "type": "synonym", "evidence": [ { "id": "P0DTC1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#names_and_taxonomy" } ] } ], "function": [ { "annotation": "Catalytic subunit of viral RNA capping enzyme which catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs (PubMed:35944563). The kinase-like NiRAN domain of NSP12 transfers RNA to the amino terminus of NSP9, forming a covalent RNA-protein intermediate (PubMed:35944563). Subsequently, the NiRAN domain transfers RNA to GDP, forming the core cap structure GpppA-RNA (PubMed:35944563). The NSP14 and NSP16 methyltransferases then add methyl groups to form functional cap structures (PubMed:35944563). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP8, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "annotation": "Cleaves the C-terminus of replicase polyprotein at 11 sites (PubMed:32321856). Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291, PubMed:32272481). Cleaves and inactivates human TRMT1, preventing tRNA guanine(26)-dimethylation of tRNAs (PubMed:37073102, PubMed:38814682, PubMed:39773525). May cleave human NLRP1 in lung epithelial cells, thereby activating the NLRP1 inflammasome pathway (PubMed:35594856). May cleave human GSDMD, triggering alternative GSDME-mediated epithelial cell death upon activation of the NLRP1 inflammasome, which may enhance the release interleukins 1B, 6, 16 and 18 (PubMed:35594856). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (PubMed:32198291, PubMed:32272481). Cleaves host STIM1 producing two functional fragments: STIM1 N-terminus, which inhibits MAVS-mediated IFNB signaling by disrupting signalosome formation, and STIM1 C-terminus, which suppresses p65-driven IFNB transcription (PubMed:41289387). Inhibits host pyroptosis through the cleavage of host gasdermin D/GSDMD (PubMed:40118151).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "PubMed", "id": "32272481", "url": "https://glygen.org/publication/PubMed/32272481" }, { "database": "PubMed", "id": "35594856", "url": "https://glygen.org/publication/PubMed/35594856" }, { "database": "PubMed", "id": "32198291", "url": "https://glygen.org/publication/PubMed/32198291" }, { "database": "PubMed", "id": "32321856", "url": "https://glygen.org/publication/PubMed/32321856" }, { "database": "PubMed", "id": "32680882", "url": "https://glygen.org/publication/PubMed/32680882" }, { "database": "PubMed", "id": "38814682", "url": "https://glygen.org/publication/PubMed/38814682" }, { "database": "PubMed", "id": "37073102", "url": "https://glygen.org/publication/PubMed/37073102" }, { "database": "PubMed", "id": "39773525", "url": "https://glygen.org/publication/PubMed/39773525" }, { "database": "PubMed", "id": "41289387", "url": "https://glygen.org/publication/PubMed/41289387" }, { "database": "PubMed", "id": "40118151", "url": "https://glygen.org/publication/PubMed/40118151" } ] }, { "annotation": "Enhances mRNA repression of the 4EHP-GYF2 complex in the host, thereby inhibiting the antiviral response and facilitating SARS-CoV-2 replication. Possibly acts in cooperation with nsp1, which induces ribosome stalling on host mRNA, triggering mRNA repression by the host 4EHP-GYF2 complex which is enhanced by nsp2.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "PubMed", "id": "35878012", "url": "https://glygen.org/publication/PubMed/35878012" } ] }, { "annotation": "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:32680882, PubMed:32979938, PubMed:33080218). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). This inhibits the integrated stress response (ISR) in the infected cell by preventing EIF2S1/eIF2-alpha phosphorylation upstream of stress granule formation and depletes host G3BP1 (PubMed:36534661). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32908316", "url": "https://glygen.org/publication/PubMed/32908316" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "33479166", "url": "https://glygen.org/publication/PubMed/33479166" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "32680882", "url": "https://glygen.org/publication/PubMed/32680882" }, { "database": "PubMed", "id": "36534661", "url": "https://glygen.org/publication/PubMed/36534661" } ] }, { "annotation": "Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" } ] }, { "annotation": "Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease (By similarity) and nsp16 2'-O-methyltransferase activities (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "annotation": "Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (LDs) (PubMed:35551511). LDs are consumed during DMV formation (PubMed:35551511). Binds to host TBK1 without affecting TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "35551511", "url": "https://glygen.org/publication/PubMed/35551511" } ] }, { "annotation": "Plays a role in viral RNA synthesis (PubMed:32277040, PubMed:32358203, PubMed:32438371, PubMed:32526208). Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers (By similarity). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP9, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32526208", "url": "https://glygen.org/publication/PubMed/32526208" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "32358203", "url": "https://glygen.org/publication/PubMed/32358203" }, { "database": "PubMed", "id": "32438371", "url": "https://glygen.org/publication/PubMed/32438371" }, { "database": "PubMed", "id": "32277040", "url": "https://glygen.org/publication/PubMed/32277040" } ] }, { "annotation": "Responsible for the cleavages located at the N-terminus of the replicase polyprotein. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication (PubMed:35551511). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Also prevents host NF-kappa-B signaling (By similarity). In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates (PubMed:32726803). Cleaves preferentially ISG15 from antiviral protein IFIH1 (MDA5), but not RIGI (PubMed:33727702). Contains an ADP-ribose hydrolase activity that binds ADP-ribose and catalyzes the removal of mono-ADP-ribose (de-MARylation), usually bound to a glutamate or aspartate (Probable) (PubMed:37242344). ADP-ribose hydrolase activity allows the virus to interfere with the host immune defenses involving poly-ADP-ribose polymerases (PARPs) (Probable). Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32733001", "url": "https://glygen.org/publication/PubMed/32733001" }, { "database": "PubMed", "id": "33727702", "url": "https://glygen.org/publication/PubMed/33727702" }, { "database": "PubMed", "id": "35551511", "url": "https://glygen.org/publication/PubMed/35551511" }, { "database": "PubMed", "id": "32578982", "url": "https://glygen.org/publication/PubMed/32578982" }, { "database": "PubMed", "id": "32726803", "url": "https://glygen.org/publication/PubMed/32726803" }, { "database": "PubMed", "id": "37242344", "url": "https://glygen.org/publication/PubMed/37242344" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "COVID-19", "description": "A disease caused by infection with severe acute respiratory syndrome coronavirus 2." }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "coronavirus disease 2019", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2 infectious disease", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-CoV-2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "betacoronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-coronavirus", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "GLY_000490", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000490" } ] } ], "snv": [], "mutagenesis": [ { "start_pos": 154, "end_pos": 157, "sequence_org": "YEDF", "sequence_mut": "AEDA", 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"url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08717", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF09401", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF09401", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF11501", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF11501", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF11633", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF11633", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF12124", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF12124", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF12379", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF12379", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF16251", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF16251", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF16348", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF16348", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19211", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19211", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19213", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19213", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19217", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19217", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19218", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19218", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "YP_009725295", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009725295", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC1-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1-1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC1", "url": "https://viral.glycomics.ku.dk/viewer/?uniprot=P0DTC1", "database": "Viral Glycome", "categories": [ "Organism-specific" ] } ], "sequence": { "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV", "length": 4405, "header": "sp|P0DTC1-1|R1A_SARS2 Isoform 1 of Replicase polyprotein 1a OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC1-1" }, "isoforms": [ { "isoform_ac": "P0DTC1-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1/entry#P0DTC1-1", "sequence": { "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV", "length": 4405, "header": "sp|P0DTC1-1|R1A_SARS2 Isoform 1 of Replicase polyprotein 1a OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC1-1" }, "locus": {} } ], "glycosylation": [], "phosphorylation": [], "glycation": [], "keywords": [ "enzyme" ], "publication": [ { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "32198291", "url": "https://glygen.org/publication/PubMed/32198291" } ] }, { "title": "Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.", "journal": "Nature", "date": "2020-06", "authors": "Jin Zhenming, Du Xiaoyu, Xu Yechun, Deng Yongqiang, Liu Meiqin, Zhao Yao, Zhang Bing, Li Xiaofeng, Zhang Leike, Peng Chao, Duan Yinkai, Yu Jing, Wang Lin, Yang Kailin, Liu Fengjiang, Jiang Rendi, Yang Xinglou, You Tian, Liu Xiaoce, Yang Xiuna, Bai Fang, Liu Hong, Liu Xiang, Guddat Luke W, Xu Wenqing, Xiao Gengfu, Qin Chengfeng, Shi Zhengli, Jiang Hualiang, Rao Zihe, Yang Haitao", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "32272481", "url": "https://glygen.org/publication/PubMed/32272481" } ] }, { "title": "Structure of the RNA-dependent RNA polymerase from COVID-19 virus.", "journal": "Science (New York, N.Y.)", "date": "2020-05-15", "authors": "Gao Yan, Yan Liming, Huang Yucen, Liu Fengjiang, Zhao Yao, Cao Lin, Wang Tao, Sun Qianqian, Ming Zhenhua, Zhang Lianqi, Ge Ji, Zheng Litao, Zhang Ying, Wang Haofeng, Zhu Yan, Zhu Chen, Hu Tianyu, Hua Tian, Zhang Bing, Yang Xiuna, Li Jun, Yang Haitao, Liu Zhijie, Xu Wenqing, Guddat Luke W, Wang Quan, Lou Zhiyong, Rao Zihe", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "32277040", "url": "https://glygen.org/publication/PubMed/32277040" } ] }, { "title": "Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.", "journal": "Science 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, McGargill Maureen A, Wolf Joshua, Thomas Paul G", "evidence": [ { "database": "IEDB", "id": "1310872", "url": "https://www.iedb.org/epitope/1310872" }, { "database": "IEDB", "id": "1311201", "url": "https://www.iedb.org/epitope/1311201" } ], "reference": [ { "type": "PubMed", "id": "35383307", "url": "https://glygen.org/publication/PubMed/35383307" } ] }, { "title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-05-09", "authors": "Titov Aleksei, Shaykhutdinova Regina, Shcherbakova Olga V, Serdyuk Yana V, Sheetikov Savely A, Zornikova Ksenia V, Maleeva Alexandra V, Khmelevskaya Alexandra, Dianov Dmitry V, Shakirova Naina T, Malko Dmitry B, Shkurnikov Maxim, Nersisyan Stepan, Tonevitsky Alexander, Khamaganova Ekaterina, Ershov Anton V, Osipova Elena Y, Nikolaev Ruslan V, Pershin Dmitry E, Vedmedskia Viktoria A, Maschan Michael, Ginanova Victoria R, Efimov Grigory A", "evidence": [ { 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R, Rossi I, Pericat D, Bagayoko S, Leon-Icaza SA, Rombouts Y, Perouzel E, Tiraby M, Zhang Q, Cicuta P, Jouanguy E, Neyrolles O, Bryant CE, Floto AR, Goujon C, Lei FZ, Martin-Blondel G, Silva S, Casanova JL, Cougoule C, Reversade B, Marcoux J, Ravet E, Meunier E", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "35594856", "url": "https://glygen.org/publication/PubMed/35594856" } ] }, { "title": "SARS-CoV-2-specific T\u00a0cell memory with common TCR\u03b1\u03b2 motifs is established in unvaccinated children who seroconvert after infection.", "journal": "Immunity", "date": "2022-07-12", "authors": "Rowntree Louise C, Nguyen Thi H O, Kedzierski Lukasz, Neeland Melanie R, Petersen Jan, Crawford Jeremy Chase, Allen Lilith F, Clemens E Bridie, Chua Brendon, McQuilten Hayley A, Minervina Anastasia A, Pogorelyy Mikhail V, Chaurasia Priyanka, Tan Hyon-Xhi, Wheatley Adam K, Jia Xiaoxiao, 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Rongtuan, Mahal Lara K, Hobman Tom C, Pelletier Jerry, Alain Tommy, Vidal Silvia M, Duchaine Thomas, Mazhab-Jafari Mohammad T, Mao Xiaojuan, Jafarnejad Seyed Mehdi, Sonenberg Nahum", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "35878012", "url": "https://glygen.org/publication/PubMed/35878012" } ] }, { "title": "The mechanism of RNA capping by SARS-CoV-2.", "journal": "Nature", "date": "2022", "authors": "Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawlowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "title": "Parallel detection of SARS-CoV-2 epitopes reveals dynamic immunodominance profiles of CD8+ T 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pathogens", "date": "2022-12", "authors": "Dolliver Stacia M, Kleer Mariel, Bui-Marinos Maxwell P, Ying Shan, Corcoran Jennifer A, Khaperskyy Denys A", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "36534661", "url": "https://glygen.org/publication/PubMed/36534661" } ] }, { "title": "SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1.", "journal": "Journal of molecular cell biology", "date": "2023-08-03", "authors": "Lu Jia-Li, Zhou Xiao-Long", "evidence": [ { "database": "UniProtKB", "id": "P0DTC1", "url": "https://www.uniprot.org/uniprotkb/P0DTC1" } ], "reference": [ { "type": "PubMed", "id": "37073102", "url": "https://glygen.org/publication/PubMed/37073102" } ] }, { "title": "Recurrent Loss of Macrodomain Activity in Host Immunity and Viral Proteins.", "journal": "Pathogens (Basel, Switzerland)", "date": "2023-05-03", "authors": 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The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.", "evidence": [] } ], "cluster_types": [], "sequence_features": { "n_linked_sites": [], "o_linked_sites": [], "snv_sites": [], "glycation_sites": [], "phosphorylation_sites": [], "sequon_annotation_sites": [ { "start_pos": 1442, "end_pos": 1444 }, { "start_pos": 1651, "end_pos": 1653 }, { "start_pos": 1719, "end_pos": 1721 }, { "start_pos": 1922, "end_pos": 1924 }, { "start_pos": 1996, "end_pos": 1998 }, { "start_pos": 2081, "end_pos": 2083 }, { "start_pos": 2102, "end_pos": 2104 }, { "start_pos": 2222, "end_pos": 2224 }, { "start_pos": 2272, "end_pos": 2274 }, { "start_pos": 2275, "end_pos": 2277 }, { "start_pos": 2405, "end_pos": 2407 }, { "start_pos": 2498, "end_pos": 2500 }, { "start_pos": 2530, "end_pos": 2532 }, { "start_pos": 2623, "end_pos": 2625 }, { "start_pos": 2682, "end_pos": 2684 }, { "start_pos": 3382, "end_pos": 3384 }, { "start_pos": 3396, "end_pos": 3398 }, { 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}, { "name": "2", "type": "synonym", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ] } ], "protein_names": [ { "name": "Spike glycoprotein", "type": "recommended", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2/entry#names_and_taxonomy" } ] }, { "name": "E2", "type": "synonym", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2/entry#names_and_taxonomy" } ] }, { "name": "Peplomer protein", "type": "synonym", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2/entry#names_and_taxonomy" } ] }, { "name": "S glycoprotein", "type": "synonym", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2/entry#names_and_taxonomy" } ] }, { "name": "surface glycoprotein", "type": "synonym", "evidence": [ { "id": "YP_009724390", "database": "RefSeq", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724390" } ] } ], "function": [ { "annotation": "Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. The major receptor is host ACE2 (PubMed:32142651, PubMed:32155444, PubMed:33607086). When S2/S2' has been cleaved, binding to the receptor triggers direct fusion at the cell membrane (PubMed:34561887). When S2/S2' has not been cleaved, binding to the receptor results in internalization of the virus by endocytosis using host TFRC and GRM2 and leading to fusion of the virion membrane with the host endosomal membrane (PubMed:32075877, PubMed:32221306, PubMed:34903715, PubMed:36779763). Alternatively, may use NRP1/NRP2 (PubMed:33082294, PubMed:33082293) and integrin as entry receptors (PubMed:35150743). The use of NRP1/NRP2 receptors may explain the tropism of the virus in human olfactory epithelial cells, which express these molecules at high levels but ACE2 at low levels (PubMed:33082293). Uses also ASGR1 as an alternative receptor in an ACE2-independent manner (PubMed:34837059). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2#function" }, { "database": "PubMed", "id": "32075877", "url": "https://glygen.org/publication/PubMed/32075877" }, { "database": "HAMAP", "id": "MF_04099", "url": "https://hamap.expasy.org/signature/MF_04099" }, { "database": "PubMed", "id": "32155444", "url": "https://glygen.org/publication/PubMed/32155444" }, { "database": "PubMed", "id": "32142651", "url": "https://glygen.org/publication/PubMed/32142651" }, { "database": "PubMed", "id": "32221306", "url": "https://glygen.org/publication/PubMed/32221306" }, { "database": "PubMed", "id": "34561887", "url": "https://glygen.org/publication/PubMed/34561887" }, { "database": "PubMed", "id": "35150743", "url": "https://glygen.org/publication/PubMed/35150743" }, { "database": "PubMed", "id": "33082294", "url": "https://glygen.org/publication/PubMed/33082294" }, { "database": "PubMed", "id": "33082293", "url": "https://glygen.org/publication/PubMed/33082293" }, { "database": "PubMed", "id": "32817270", "url": "https://glygen.org/publication/PubMed/32817270" }, { "database": "PubMed", "id": "34903715", "url": "https://glygen.org/publication/PubMed/34903715" }, { "database": "PubMed", "id": "36779763", "url": "https://glygen.org/publication/PubMed/36779763" }, { "database": "PubMed", "id": "34837059", "url": "https://glygen.org/publication/PubMed/34837059" } ] }, { "annotation": "Precursor of the fusion protein processed in the biosynthesis of the S protein and the formation of virus particle. Mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. Contains two viral fusion peptides that are unmasked after cleavage. The S2/S2' cleavage occurs during virus entry at the cell membrane by host TMPRSS2 (PubMed:32142651) or during endocytosis by host CSTL (PubMed:32703818, PubMed:34159616). In either case, this triggers an extensive and irreversible conformational change leading to fusion of the viral envelope with the cellular cytoplasmic membrane, releasing viral genomic RNA into the host cell cytoplasm (PubMed:34561887). Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of the viral and target cell membranes, the coiled coil regions (heptad repeats) adopt a trimer-of-hairpins structure and position the fusion peptide in close proximity to the C-terminal region of the ectodomain. Formation of this structure appears to promote apposition and subsequent fusion of viral and target cell membranes.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2#function" }, { "database": "HAMAP", "id": "MF_04099", "url": "https://hamap.expasy.org/signature/MF_04099" }, { "database": "PubMed", "id": "34561887", "url": "https://glygen.org/publication/PubMed/34561887" }, { "database": "PubMed", "id": "32703818", "url": "https://glygen.org/publication/PubMed/32703818" }, { "database": "PubMed", "id": "34159616", "url": "https://glygen.org/publication/PubMed/34159616" } ] }, { "annotation": "Subunit of the fusion protein that is processed upon entry into the host cell. Mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. Contains a viral fusion peptide that is unmasked after S2 cleavage. This cleavage can occur at the cell membrane by host TMPRSS2 or during endocytosis by host CSTL (PubMed:32703818, PubMed:34159616). In either case, this triggers an extensive and irreversible conformational change that leads to fusion of the viral envelope with the cellular cytoplasmic membrane, releasing viral genomic RNA into the host cell cytoplasm (PubMed:34561887). Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of the viral and target cell membranes, the coiled coil regions (heptad repeats) adopt a trimer-of-hairpins structure and position the fusion peptide in close proximity to the C-terminal region of the ectodomain. Formation of this structure appears to promote apposition and subsequent fusion of viral and target cell membranes.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2#function" }, { "database": "HAMAP", "id": "MF_04099", "url": "https://hamap.expasy.org/signature/MF_04099" }, { "database": "PubMed", "id": "34561887", "url": "https://glygen.org/publication/PubMed/34561887" }, { "database": "PubMed", "id": "32703818", "url": "https://glygen.org/publication/PubMed/32703818" }, { "database": "PubMed", "id": "34159616", "url": "https://glygen.org/publication/PubMed/34159616" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "COVID-19", "description": "A disease caused by infection with severe acute respiratory syndrome coronavirus 2." }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "coronavirus disease 2019", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2 infectious disease", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-CoV-2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "betacoronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-coronavirus", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "GLY_000490", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000490" } ] } ], "snv": [], "mutagenesis": [ { "start_pos": 121, "end_pos": 121, "sequence_org": "N", "sequence_mut": "Q", "comment": "Partial loss of biliverdin affinity.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "33888467", "url": "https://glygen.org/publication/PubMed/33888467" } ] }, { "start_pos": 1269, "end_pos": 1269, "sequence_org": "K", "sequence_mut": "A", "comment": "Complete loss of COPI binding and increase in cell fusion.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34504087", "url": "https://glygen.org/publication/PubMed/34504087" } ] }, { "start_pos": 1271, "end_pos": 1271, "sequence_org": "H", "sequence_mut": "K", "comment": "Improved COPI binding, reduced cell fusion and reduced levels of S1/S2 cleavage.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34504087", "url": "https://glygen.org/publication/PubMed/34504087" } ] }, { "start_pos": 190, "end_pos": 190, "sequence_org": "R", "sequence_mut": "K", "comment": "Partial loss of biliverdin affinity.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "33888467", "url": "https://glygen.org/publication/PubMed/33888467" } ] }, { "start_pos": 234, "end_pos": 234, "sequence_org": "N", "sequence_mut": "Q", "comment": "Increased resistance to neutralizing antibodies.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 331, "end_pos": 331, "sequence_org": "N", "sequence_mut": "Q", "comment": "Reduced viral infectivity.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 343, "end_pos": 343, "sequence_org": "N", "sequence_mut": "Q", "comment": "Reduced viral infectivity.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 452, "end_pos": 452, "sequence_org": "L", "sequence_mut": "R", "comment": "Increased resistance to neutralizing antibodies. Decreases HLA binding to NF9 epitope. Increased binding affinity to human ACE2.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" }, { "database": "PubMed", "id": "34171266", "url": "https://glygen.org/publication/PubMed/34171266" } ] }, { "start_pos": 453, "end_pos": 453, "sequence_org": "Y", "sequence_mut": "F", "comment": "Decreased HLA binding to NF9 epitope. Increased binding affinity to human ACE2.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34171266", "url": "https://glygen.org/publication/PubMed/34171266" } ] }, { "start_pos": 475, "end_pos": 475, "sequence_org": "A", "sequence_mut": "V", "comment": "Increased resistance to neutralizing antibodies.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 483, "end_pos": 483, "sequence_org": "V", "sequence_mut": "A", "comment": "Increased resistance to neutralizing antibodies.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 484, "end_pos": 484, "sequence_org": "E", "sequence_mut": "D", "comment": "Increased replication in human TMEM106B overexpressing cells.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "37421949", "url": "https://glygen.org/publication/PubMed/37421949" } ] }, { "start_pos": 490, "end_pos": 490, "sequence_org": "F", "sequence_mut": "L", "comment": "Increased resistance to neutralizing antibodies and human covalescent sera neutralization.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 493, "end_pos": 493, "sequence_org": "Q", "sequence_mut": "N", "comment": "Reduced host ACE2-binding affinity in vitro.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32225175", "url": "https://glygen.org/publication/PubMed/32225175" } ] }, { "start_pos": 493, "end_pos": 493, "sequence_org": "Q", "sequence_mut": "Y", "comment": "Reduced host ACE2-binding affinity in vitro.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32225175", "url": "https://glygen.org/publication/PubMed/32225175" } ] }, { "start_pos": 501, "end_pos": 501, "sequence_org": "N", "sequence_mut": "T", "comment": "Reduced host ACE2-binding affinity in vitro.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32225175", "url": "https://glygen.org/publication/PubMed/32225175" } ] }, { "start_pos": 501, "end_pos": 501, "sequence_org": "N", "sequence_mut": "Y", "comment": "Increased binding affinity to human ACE2.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34171266", "url": "https://glygen.org/publication/PubMed/34171266" } ] }, { "start_pos": 519, "end_pos": 519, "sequence_org": "H", "sequence_mut": "P", "comment": "Increased resistance to human covalescent sera neutralization.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32730807", "url": "https://glygen.org/publication/PubMed/32730807" } ] }, { "start_pos": 614, "end_pos": 614, "sequence_org": "D", "sequence_mut": "G", "comment": "Increase of pseudotyped VSV particle production ex vivo. Increase of viral load in hamster upper respiratory tract. Produces more infectious particles when cultured in primary human epithelial cells; increases replication and transmissibility in hamsters and ferrets.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32697968", "url": "https://glygen.org/publication/PubMed/32697968" }, { "database": "PubMed", "id": "33636719", "url": "https://glygen.org/publication/PubMed/33636719" }, { "database": "PubMed", "id": "33106671", "url": "https://glygen.org/publication/PubMed/33106671" } ] }, { "start_pos": 673, "end_pos": 673, "sequence_org": "S", "sequence_mut": "A", "comment": "No effect on O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 676, "end_pos": 676, "sequence_org": "T", "sequence_mut": "A", "comment": "Partial loss of O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 678, "end_pos": 678, "sequence_org": "T", "sequence_mut": "A", "comment": "Complete loss of O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 679, "end_pos": 684, "sequence_org": "NSPRRA", "sequence_mut": "IL", "comment": "About 50% stronger entry efficiency in Vero E6 cells while 30% weaker entry efficiency in hACE2-expressing BHK cells.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32155444", "url": "https://glygen.org/publication/PubMed/32155444" } ] }, { "start_pos": 680, "end_pos": 680, "sequence_org": "S", "sequence_mut": "A", "comment": "No effect on O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 681, "end_pos": 681, "sequence_org": "P", "sequence_mut": "A", "comment": "Complete loss of O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 681, "end_pos": 681, "sequence_org": "P", "sequence_mut": "H", "comment": "Complete loss of O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 681, "end_pos": 681, "sequence_org": "P", "sequence_mut": "R", "comment": "Complete loss of O-glycosylation by host GALNT1.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "start_pos": 681, "end_pos": 684, "sequence_org": "PRRA", "sequence_mut": "RRRK", "comment": "Optimized cleavage by host furin.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32362314", "url": "https://glygen.org/publication/PubMed/32362314" } ] }, { "start_pos": 682, "end_pos": 684, "sequence_org": "RRA", "sequence_mut": "", "comment": "Complete loss of cleavage by host furin.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32362314", "url": "https://glygen.org/publication/PubMed/32362314" } ] }, { "start_pos": 682, "end_pos": 685, "sequence_org": "RRAR", "sequence_mut": "SRAG", "comment": "Stabilization in prefusion state (in vaccine Ad26.COV2.S/Janssen Pharmaceutical).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34322129", "url": "https://glygen.org/publication/PubMed/34322129" } ] }, { "start_pos": 684, "end_pos": 684, "sequence_org": "A", "sequence_mut": "K", "comment": "Partial improvement of cleavage by host furin.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32703818", "url": "https://glygen.org/publication/PubMed/32703818" } ] }, { "start_pos": 684, "end_pos": 684, "sequence_org": "A", "sequence_mut": "R", "comment": "Partial improvement of cleavage by host furin.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32703818", "url": "https://glygen.org/publication/PubMed/32703818" } ] }, { "start_pos": 69, "end_pos": 70, "sequence_org": "HV", "sequence_mut": "", "comment": "Increased incorporation of cleaved spike into virions.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34166617", "url": "https://glygen.org/publication/PubMed/34166617" } ] }, { "start_pos": 986, "end_pos": 987, "sequence_org": "KV", "sequence_mut": "PP", "comment": "Stabilization in prefusion state (in vaccine BNT162b2/Pfizer-Biontech, vaccine mRNA-1273/Moderna, vaccine Ad26.COV2.S/Janssen Pharmaceutical).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34322129", "url": "https://glygen.org/publication/PubMed/34322129" } ] } ], "expression_tissue": [], "expression_disease": [], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "gene": [ { "name": "S", "url": "https://www.uniprot.org/uniprotkb/P0DTC2", "locus": { "chromosome": "NC_045512.2", "start_pos": 25384, "end_pos": 21563, "strand": "-", "evidence": [ { "database": "Ensembl Gene", "id": "GU280_gp02", "url": "https://covid-19.ensembl.org/Sars_cov_2/Gene/Summary?g=GU280_gp02" } ] } } ], "crossref": [ { "id": "43740568", "url": "https://www.ncbi.nlm.nih.gov/gene/43740568", "database": "GeneID", "categories": [ 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1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G54417MJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G55382TU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G56610MH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G64162JC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G67367OT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" } ] }, { "glytoucan_ac": "G68318VE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" } ] }, { "glytoucan_ac": "G69364JQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G74724QE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G80475RE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-T-after-R2", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G80735OA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 2", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G82364UA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32518941", "database": "PubMed", 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Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G88725PI", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G93579XB", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Patient immunopeptidomic samples. Antibody L243. Patient reference C2.", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G94854LT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G98596OT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 1173, "start_aa": "Asn", "end_pos": 1173, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1173", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", 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"https://glygen.org/publication/DOI/10.3390/v13040551" }, { "id": "2952", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2952" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true, "automatic_literature_mining": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GlcNAc...) threonine;O-GlcNAcylation", "icn3d_view": {}, "start_pos": 678, "start_aa": "Thr", "end_pos": 678, "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr678", "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2#ptm_processing" }, { "id": "34732583", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34732583" }, { "id": "33406838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33406838" }, { "id": "", "database": "GlyGen", "url": "https://data.glygen.org/" }, { "id": "32676595", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32676595" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 679, "start_aa": "Asn", "end_pos": 679, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn679", "evidence": [ { "id": "35575289", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35575289" }, { "id": "", "database": "GlyGen", "url": "https://data.glygen.org/" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7XIY&bu=0&command=select+.C:709;+center+selection;+zoom+selection" }, "start_pos": 703, "start_aa": "Asn", "end_pos": 703, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn703", "evidence": [ { "id": "7XIY", "database": "PDB", "url": "https://www.rcsb.org/structure/7XIY" }, { "id": "7XIY", "database": "PDB", "url": "https://www.rcsb.org/structure/7XIY" }, { "id": "7Y1Z", "database": "PDB", "url": "https://www.rcsb.org/structure/7Y1Z" }, { "id": "7Y1Z", "database": "PDB", "url": "https://www.rcsb.org/structure/7Y1Z" }, { "id": "7Y20", "database": "PDB", "url": "https://www.rcsb.org/structure/7Y20" }, { "id": "7Y20", "database": "PDB", "url": "https://www.rcsb.org/structure/7Y20" }, { "id": "7XIY|C|709", "database": "", "url": "" }, { "id": "7XIY|B|709", "database": "", "url": "" }, { "id": "7XIY|A|709", "database": "", "url": "" }, { "id": "7Y1Z|A|709", "database": "", "url": "" }, { "id": "7Y20|B|709", "database": "", "url": "" } ] }, { "glytoucan_ac": "G00406II", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G05724UK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G08011QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G08293MJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G10256JP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G10339FR", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G15486FH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G16407EV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-before-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G20956ZV", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G21726WW", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R2", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" } ] }, { "glytoucan_ac": "G22040QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G22768VO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8CYB&bu=0&command=select+.A:709;+center+selection;+zoom+selection" }, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "8CYB", "database": "PDB", "url": "https://www.rcsb.org/structure/8CYB" }, { "id": "8CYB", "database": "PDB", "url": "https://www.rcsb.org/structure/8CYB" }, { "id": "8CYB|A|709", "database": "", "url": "" } ] }, { "glytoucan_ac": "G23453IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G25637MV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G25987BV", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G26759AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G27622TD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G28681TP", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G28997IA", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G32104JU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G35029YA", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-before-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G39188ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G39446WN", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G44215PV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G45504EY", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "SARS-CoV-2 S protein", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1101/2020.04.01.020966", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2020.04.01.020966" } ] }, { "glytoucan_ac": "G46687AB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G49874UX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G53434XO", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G57317CE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R2", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" } ] }, { "glytoucan_ac": "G57776ZU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-TG-before-R2", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" } ] }, { "glytoucan_ac": "G59937CP", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-LC", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G64527OM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G66538GV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G67324HN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G68318VE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G70101JE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G76613WN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G80475RE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-AC", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G82364UA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-before-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G83555HU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "S2P-LC", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33064451", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33064451" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1021/acs.analchem.0c03301", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.0c03301" }, { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G88725PI", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Identified intact N-glycopeptides with noted commentS-G-after-R1", "icn3d_view": {}, "start_pos": 709, "start_aa": "Asn", "end_pos": 709, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn709", "evidence": [ { "id": "33077685", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33077685" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1074/mcp.RA120.002295", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.RA120.002295" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": 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Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G10773YW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G14260UH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" } ] }, { "glytoucan_ac": "G14994KB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G15486FH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G16407EV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G20956ZV", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G21643DJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G22573RC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=9BBK&bu=0&command=select+.B:717;+center+selection;+zoom+selection" }, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "9BBK", "database": "PDB", "url": "https://www.rcsb.org/structure/9BBK" }, { "id": "9BBK", "database": "PDB", "url": "https://www.rcsb.org/structure/9BBK" }, { "id": "9BD9", "database": "PDB", "url": "https://www.rcsb.org/structure/9BD9" }, { "id": "9BD9", "database": "PDB", "url": "https://www.rcsb.org/structure/9BD9" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "9BBK|B|717", "database": "", "url": "" }, { "id": "9BD9|B|717", "database": "", "url": "" }, { "id": "9BEA|C|717", "database": "", "url": "" } ] }, { "glytoucan_ac": "G22768VO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7TEI&bu=0&command=select+.C:717;+center+selection;+zoom+selection" }, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "7TEI", "database": "PDB", "url": "https://www.rcsb.org/structure/7TEI" }, { "id": "7TEI", "database": "PDB", "url": "https://www.rcsb.org/structure/7TEI" }, { "id": "7TF8", "database": "PDB", "url": "https://www.rcsb.org/structure/7TF8" }, { "id": "7TF8", "database": "PDB", "url": "https://www.rcsb.org/structure/7TF8" }, { "id": "7WUH", "database": "PDB", "url": "https://www.rcsb.org/structure/7WUH" }, { "id": "7WUH", "database": "PDB", "url": "https://www.rcsb.org/structure/7WUH" }, { "id": "8EPN", "database": "PDB", "url": "https://www.rcsb.org/structure/8EPN" }, { "id": "8EPN", "database": "PDB", "url": "https://www.rcsb.org/structure/8EPN" }, { "id": "8CYB", "database": "PDB", "url": "https://www.rcsb.org/structure/8CYB" }, { "id": "8CYB", "database": "PDB", "url": "https://www.rcsb.org/structure/8CYB" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "7TEI|C|717", "database": "", "url": "" }, { "id": "7TEI|B|717", "database": "", "url": "" }, { "id": "7TEI|A|717", "database": "", "url": "" }, { "id": "7TF8|B|717", "database": "", "url": "" }, { "id": "7TF8|C|717", "database": "", "url": "" }, { "id": "7WUH|C|717", "database": "", "url": "" }, { "id": "8EPN|C|717", "database": "", "url": "" }, { "id": "8EPN|B|717", "database": "", "url": "" }, { "id": "8EPN|A|717", "database": "", "url": "" }, { "id": "8CYB|C|717", "database": "", "url": "" }, { "id": "8CYB|A|717", "database": "", "url": "" }, { "id": "9BEA|A|717", "database": "", "url": "" } ] }, { "glytoucan_ac": "G23294PN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G23453IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G23863VK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G25987BV", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G28681TP", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G29880MM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G30799SW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G33609NS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G34029GR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 3", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G35029YA", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 1", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G39188ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G39446WN", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G46687AB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G50045TK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G50073PQ", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 3", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G53434XO", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G54600FO", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 1", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G57776ZU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G58802FE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 3", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G59937CP", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G60145BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G60177UT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G66538GV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G66766XF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G67324HN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" } ] }, { "glytoucan_ac": "G70101JE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G72735IY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G74430RZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G79568CQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G80475RE", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 1", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Biological Replicate 1", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" }, { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" } ] }, { "glytoucan_ac": "G81315DD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=6ZOW&bu=0&command=select+.B:717;+center+selection;+zoom+selection" }, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "6ZOW", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZOW" }, { "id": "6ZOW", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZOW" }, { "id": "6ZP5", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZP5" }, { "id": "6ZP5", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZP5" }, { "id": "6ZP7", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZP7" }, { "id": "6ZP7", "database": "PDB", "url": "https://www.rcsb.org/structure/6ZP7" }, { "id": "7TF8", "database": "PDB", "url": "https://www.rcsb.org/structure/7TF8" }, { "id": "7TF8", "database": "PDB", "url": "https://www.rcsb.org/structure/7TF8" }, { "id": "7TL1", "database": "PDB", "url": "https://www.rcsb.org/structure/7TL1" }, { "id": "7TL1", "database": "PDB", "url": "https://www.rcsb.org/structure/7TL1" }, { "id": "9B8F", "database": "PDB", "url": "https://www.rcsb.org/structure/9B8F" }, { "id": "9B8F", "database": "PDB", "url": "https://www.rcsb.org/structure/9B8F" }, { "id": "9B9U", "database": "PDB", "url": "https://www.rcsb.org/structure/9B9U" }, { "id": "9B9U", "database": "PDB", "url": "https://www.rcsb.org/structure/9B9U" }, { "id": "9BBK", "database": "PDB", "url": "https://www.rcsb.org/structure/9BBK" }, { "id": "9BBK", "database": "PDB", "url": "https://www.rcsb.org/structure/9BBK" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "9BEA", "database": "PDB", "url": "https://www.rcsb.org/structure/9BEA" }, { "id": "6ZOW|B|717", "database": "", "url": "" }, { "id": "6ZOW|A|717", "database": "", "url": "" }, { "id": "6ZP5|B|538", "database": "", "url": "" }, { "id": "6ZP5|A|690", "database": "", "url": "" }, { "id": "6ZP7|B|717", "database": "", "url": "" }, { "id": "6ZP7|A|717", "database": "", "url": "" }, { "id": "7TF8|A|717", "database": "", "url": "" }, { "id": "7TL1|A|717", "database": "", "url": "" }, { "id": "9B8F|C|717", "database": "", "url": "" }, { "id": "9B8F|A|717", "database": "", "url": "" }, { "id": "9B9U|B|717", "database": "", "url": "" }, { "id": "9BBK|C|717", "database": "", "url": "" }, { "id": "9BEA|B|717", "database": "", "url": "" } ] }, { "glytoucan_ac": "G82119TF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32363391", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32363391" }, { "id": "2838", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2838" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G82364UA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Glycan database GlycomeDB; gLabel embedded in pGlyco2.0; Byonic (N-glycan 38 insect database)", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" } ] }, { "glytoucan_ac": "G82463GQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G83555HU", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "glytoucan_ac": "G84452RH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G84820NF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "2840", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2840" } ] }, { "glytoucan_ac": "G86408JD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "32518941", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32518941" }, { "id": "2839", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2839" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "Elastase digestion of purified S protein, providing glycopeptide identification metrics from Byonic search. Expression construct included residues 1\u22121208 of the SARS-CoV-2 S (GenBank: MN908947) with proline substitutions at residues 986 and 987, a \u201cGSAS\u201d substitution at the furin cleavage site (residues 682\u2013685), a C-terminal T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag and an 8XHisTag.", "icn3d_view": {}, "start_pos": 717, "start_aa": "Asn", "end_pos": 717, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn717", "evidence": [ { "id": "34004174", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34004174" }, { "id": "GLY_000479", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000479" }, { "id": "10.1016/j.celrep.2021.109179", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1016/j.celrep.2021.109179" }, { "id": "32366695", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32366695" }, { "id": "10.1126/science.abb9983", "database": "DOI", "url": 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SARS-CoV-2", "journal": "bioRxiv", "date": "2020", "authors": "Shajahan A., Supekar N.T., Gleinich A.S., Azadi P.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000479", "url": "http://data.glygen.org/GLY_000479" } ], "reference": [ { "type": "DOI", "id": "10.1101/2020.04.01.020966", "url": "https://glygen.org/publication/DOI/10.1101/2020.04.01.020966" } ] }, { "title": "Site-specific glycan analysis of the SARS-CoV-2 spike", "journal": "Science", "date": "2020", "authors": "Watanabe Y., Allen J.D., Wrapp D., McLellan J.S., Crispin M.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000479", "url": "http://data.glygen.org/GLY_000479" } ], "reference": [ { "type": "DOI", "id": "10.1126/science.abb9983", "url": "https://glygen.org/publication/DOI/10.1126/science.abb9983" } ] }, { "title": "Site-Specific O-Glycosylation Analysis of SARS-CoV-2 Spike Protein Produced in Insect and Human Cells", "journal": "Viruses", "date": "2021", "authors": "Bagdonaite I., Thompson A.J., Wang X., S\u00f8gaard M., Fougeroux C., Frank M., Diedrich J.K., Yates J.R. 3rd, Salanti A., Vakhrushev S.Y., Paulson J.C., Wandall H.H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000479", "url": "http://data.glygen.org/GLY_000479" } ], "reference": [ { "type": "DOI", "id": "10.3390/v13040551", "url": "https://glygen.org/publication/DOI/10.3390/v13040551" } ] }, { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32075877", "url": "https://glygen.org/publication/PubMed/32075877" } ] }, { "title": "Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32132184", "url": "https://glygen.org/publication/PubMed/32132184" } ] }, { "title": "SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.", "journal": 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glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV.", "journal": "Nature communications", "date": "2020", "authors": "Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, Guo L, Guo R, Chen T, Hu J, Xiang Z, Mu Z, Chen X, Chen J, Hu K, Jin Q, Wang J, Qian Z", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32221306", "url": "https://glygen.org/publication/PubMed/32221306" } ] }, { "title": "Structural basis of receptor recognition by SARS-CoV-2.", "journal": "Nature", "date": "2020", "authors": "Shang J, Ye G, Shi K, Wan Y, Luo C, Aihara H, Geng Q, Auerbach A, Li F", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32225175", "url": "https://glygen.org/publication/PubMed/32225175" } ] }, { "title": "Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.", "journal": "Nature", "date": "2020", "authors": "Lan Jun, Ge Jiwan, Yu Jinfang, Shan Sisi, Zhou Huan, Fan Shilong, Zhang Qi, Shi Xuanling, Wang Qisheng, Zhang Linqi, Wang Xinquan", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32225176", "url": "https://glygen.org/publication/PubMed/32225176" } ] }, { "title": "A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV.", "journal": "Science", "date": "2020", "authors": "Yuan Meng, Wu Nicholas C, Zhu Xueyong, Lee Chang-Chun D, So Ray T Y, Lv Huibin, Mok Chris K P, Wilson Ian A", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "32245784", "url": "https://glygen.org/publication/PubMed/32245784" } ] }, { "title": "A Multibasic Cleavage Site in the Spike Protein of 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against SARS-COV-2 Spike Protein and Epitope Mapping.", "journal": "Journal of immunology research", "date": "2020", "authors": "Lu Yan, Wang Yajun, Zhang Zhen, Huang Jingliang, Yao Meicun, Huang Guobin, Ge Yuanyuan, Zhang Peichun, Huang Huaxin, Wang Yong, Li Huiliang, Wang Wen", "evidence": [ { "database": "IEDB", "id": "1309137", "url": "https://www.iedb.org/epitope/1309137" }, { "database": "IEDB", "id": "1311314", "url": "https://www.iedb.org/epitope/1311314" }, { "database": "IEDB", "id": "1311330", "url": "https://www.iedb.org/epitope/1311330" }, { "database": "IEDB", "id": "1311393", "url": "https://www.iedb.org/epitope/1311393" }, { "database": "IEDB", "id": "1311461", "url": "https://www.iedb.org/epitope/1311461" } ], "reference": [ { "type": "PubMed", "id": "33134398", "url": "https://glygen.org/publication/PubMed/33134398" } ] }, { "title": "Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein.", "journal": "ACS central science", "date": "2020-10-28", "authors": "Casalino Lorenzo, Gaieb Zied, Goldsmith Jory A, Hjorth Christy K, Dommer Abigail C, Harbison Aoife M, Fogarty Carl A, Barros Emilia P, Taylor Bryn C, McLellan Jason S, Fadda Elisa, Amaro Rommie E", "evidence": [ { "database": "PubMed", "id": "33140034", "url": "https://glygen.org/publication/PubMed/33140034" } ], "reference": [ { "type": "PubMed", "id": "33140034", "url": "https://glygen.org/publication/PubMed/33140034" } ] }, { "title": "SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH 3rd, Leist SR, Schafer A, Nakajima N, Takahashi K, Lee RE, Mascenik TM, Graham R, Edwards CE, Tse LV, Okuda K, Markmann AJ, Bartelt L, de Silva A, Margolis DM, Boucher RC, Randell SH, Suzuki T, Gralinski LE, Kawaoka Y, Baric RS", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": 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Chem.", "date": "2020", "authors": "Boson Bertrand, Legros Vincent, Zhou Bingjie, Siret Eglantine, Mathieu Cyrille, Cosset Fran\u00e7ois-Lo\u00efc, Lavillette Dimitri, Denolly Sol\u00e8ne", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "33229438", "url": "https://glygen.org/publication/PubMed/33229438" } ] }, { "title": "T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research.", "journal": "Journal of cellular and molecular medicine", "date": "2021-01", "authors": "Chen Ziwei, Ruan Pinglang, Wang Lili, Nie Xinmin, Ma Xuejun, Tan Yurong", "evidence": [ { "database": "IEDB", "id": "1319519", "url": "https://www.iedb.org/epitope/1319519" } ], "reference": [ { "type": "PubMed", "id": "33325143", "url": "https://glygen.org/publication/PubMed/33325143" } ] }, { "title": "PD-1-Expressing SARS-CoV-2-Specific CD8+ T Cells Are Not 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Chemie (International ed. in English)", "date": "2021-06-01", "authors": "Ye Farong, Zhao Jie, Xu Peng, Liu Xinliang, Yu Jing, Shangguan Wei, Liu Jiazhi, Luo Xiaosheng, Li Cheng, Ying Tianlei, Wang Jing, Yu Biao, Wang Ping", "evidence": [ { "database": "PubMed", "id": "33709491", "url": "https://glygen.org/publication/PubMed/33709491" } ], "reference": [ { "type": "PubMed", "id": "33709491", "url": "https://glygen.org/publication/PubMed/33709491" } ] }, { "title": "Assessment of SARS-CoV-2 specific CD4(+) and CD8 (+) T cell responses using MHC class I and II tetramers.", "journal": "Vaccine", "date": "2021-04-08", "authors": "Poluektov Yuri, George Marybeth, Daftarian Pirouz, Delcommenne Marc C", "evidence": [ { "database": "IEDB", "id": "1310865", "url": "https://www.iedb.org/epitope/1310865" } ], "reference": [ { "type": "PubMed", "id": "33744048", "url": "https://glygen.org/publication/PubMed/33744048" } ] }, { "title": "Potent SARS-CoV-2 neutralizing antibodies directed against 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Hartmann Rune, \u00d8stergaard Lars, S\u00f8gaard Ole S, Schleimann Mariane H, Tolstrup Martin", "evidence": [ { "database": "IEDB", "id": "16156", "url": "https://www.iedb.org/epitope/16156" }, { "database": "IEDB", "id": "44814", "url": "https://www.iedb.org/epitope/44814" }, { "database": "IEDB", "id": "54680", "url": "https://www.iedb.org/epitope/54680" }, { "database": "IEDB", "id": "69657", "url": "https://www.iedb.org/epitope/69657" }, { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" } ], "reference": [ { "type": "PubMed", "id": "34098342", "url": "https://glygen.org/publication/PubMed/34098342" } ] }, { "title": "Comparative Immunomodulatory Evaluation of the Receptor Binding Domain of the SARS-CoV-2 Spike Protein; a Potential Vaccine Candidate Which Imparts Potent Humoral and Th1 Type Immune Response in a Mouse Model.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Shrivastava Tripti, Singh Balwant, Rizvi Zaigham Abbas, Verma Rohit, Goswami Sandeep, Vishwakarma Preeti, Jakhar Kamini, Sonar Sudipta, Mani Shailendra, Bhattacharyya Sankar, Awasthi Amit, Surjit Milan", "evidence": [ { "database": "PubMed", "id": "34108961", "url": "https://glygen.org/publication/PubMed/34108961" } ], "reference": [ { "type": "PubMed", "id": "34108961", "url": "https://glygen.org/publication/PubMed/34108961" } ] }, { "title": "TMPRSS2 expression dictates the entry route used by SARS-CoV-2 to infect host cells.", "journal": "The EMBO journal", "date": "2021", "authors": "Koch J, Uckeley ZM, Doldan P, Stanifer M, Boulant S, Lozach PY", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "34159616", "url": "https://glygen.org/publication/PubMed/34159616" } ] }, { "title": "Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals.", "journal": "Scientific reports", "date": "2021-06-23", "authors": "Mahajan Swapnil, Kode Vasumathi, Bhojak Keshav, Karunakaran Coral, Lee Kayla, Manoharan Malini, Ramesh Athulya, Hv Sudheendra, Srivastava Ankita, Sathian Rekha, Khan Tahira, Kumar Prasanna, Gupta Ravi, Chakraborty Papia, Chaudhuri Amitabha", "evidence": [ { "database": "IEDB", "id": "1071575", "url": "https://www.iedb.org/epitope/1071575" }, { "database": "IEDB", "id": "1074201", "url": "https://www.iedb.org/epitope/1074201" }, { "database": "IEDB", "id": "1074214", "url": "https://www.iedb.org/epitope/1074214" }, { "database": "IEDB", "id": "1309117", "url": "https://www.iedb.org/epitope/1309117" }, { "database": "IEDB", "id": "1310437", "url": "https://www.iedb.org/epitope/1310437" }, { "database": "IEDB", "id": "1310448", "url": "https://www.iedb.org/epitope/1310448" }, { "database": "IEDB", "id": "1310503", "url": "https://www.iedb.org/epitope/1310503" }, { "database": "IEDB", "id": "1310747", "url": 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"https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "34166617", "url": "https://glygen.org/publication/PubMed/34166617" } ] }, { "title": "SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity.", "journal": "Cell host & microbe", "date": "2021", "authors": "Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, Ikeda T, Nakagawa S, Ueno T, Sato K", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "34171266", "url": "https://glygen.org/publication/PubMed/34171266" } ] }, { "title": "Profiling SARS-CoV-2 HLA-I peptidome reveals T\u00a0cell epitopes from out-of-frame ORFs.", "journal": "Cell", "date": "2021-07-22", "authors": "Weingarten-Gabbay Shira, Klaeger Susan, Sarkizova Siranush, Pearlman Leah R, Chen Da-Yuan, Gallagher Kathleen M E, Bauer Matthew R, Taylor Hannah B, Dunn W Augustine, Tarr Christina, Sidney John, Rachimi Suzanna, Conway Hasahn L, Katsis Katelin, Wang Yuntong, Leistritz-Edwards Del, Durkin Melissa R, Tomkins-Tinch Christopher H, Finkel Yaara, Nachshon Aharon, Gentili Matteo, Rivera Keith D, Carulli Isabel P, Chea Vipheaviny A, Chandrashekar Abishek, Bozkus Cansu Cimen, Carrington Mary, , Bhardwaj Nina, Barouch Dan H, Sette Alessandro, Maus Marcela V, Rice Charles M, Clauser Karl R, Keskin Derin B, Pregibon Daniel C, Hacohen Nir, Carr Steven A, Abelin Jennifer G, Saeed Mohsan, Sabeti Pardis C", "evidence": [ { "database": "IEDB", "id": "44814", "url": "https://www.iedb.org/epitope/44814" }, { "database": "IEDB", "id": "1074876", "url": "https://www.iedb.org/epitope/1074876" }, { "database": "IEDB", "id": "1323406", "url": "https://www.iedb.org/epitope/1323406" }, { "database": "IEDB", "id": "1332221", "url": "https://www.iedb.org/epitope/1332221" }, { "database": "IEDB", "id": "1332509", "url": "https://www.iedb.org/epitope/1332509" }, { "database": "IEDB", "id": "1332861", "url": "https://www.iedb.org/epitope/1332861" }, { "database": "IEDB", "id": "1334182", "url": "https://www.iedb.org/epitope/1334182" }, { "database": "IEDB", "id": "1625928", "url": "https://www.iedb.org/epitope/1625928" } ], "reference": [ { "type": "PubMed", "id": "34171305", "url": "https://glygen.org/publication/PubMed/34171305" } ] }, { "title": "A Murine CD8+ T Cell Epitope Identified in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein.", "journal": "Vaccines", "date": "2021-06-11", "authors": "Yang Jihyun, Kim Eunjin, Lee Jong-Soo, Poo Haryoung", "evidence": [ { "database": "IEDB", "id": "1397510", "url": "https://www.iedb.org/epitope/1397510" } ], "reference": [ { "type": "PubMed", "id": "34208032", "url": "https://glygen.org/publication/PubMed/34208032" } ] }, { "title": "CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients.", "journal": "Science immunology", "date": "2021-07-01", "authors": "Mallajosyula Vamsee, Ganjavi Conner, Chakraborty Saborni, McSween Alana M, Pavlovitch-Bedzyk Ana Jimena, Wilhelmy Julie, Nau Allison, Manohar Monali, Nadeau Kari C, Davis Mark M", "evidence": [ { "database": "IEDB", "id": "16156", "url": "https://www.iedb.org/epitope/16156" }, { "database": "IEDB", "id": "54507", "url": "https://www.iedb.org/epitope/54507" }, { "database": "IEDB", "id": "69657", "url": "https://www.iedb.org/epitope/69657" }, { "database": "IEDB", "id": "1309137", "url": "https://www.iedb.org/epitope/1309137" }, { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" }, { "database": "IEDB", "id": "1319519", "url": "https://www.iedb.org/epitope/1319519" } ], "reference": [ { "type": "PubMed", "id": "34210785", "url": "https://glygen.org/publication/PubMed/34210785" } ] }, { "title": "SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern.", "journal": "Science (New York, N.Y.)", "date": "2021", "authors": "McCallum M, Bassi J, De Marco A, Chen A, Walls AC, Di Iulio J, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Sprouse KR, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "34210893", "url": "https://glygen.org/publication/PubMed/34210893" } ] }, { "title": "Identification of cross-reactive CD8+ T cell receptors with high functional avidity to a SARS-CoV-2 immunodominant epitope and its natural mutant variants.", "journal": "Genes & diseases", "date": "2022-01", "authors": "Hu Chao, Shen Meiying, Han Xiaojian, Chen Qian, Li Luo, Chen Siyin, Zhang Jing, Gao Fengxia, Wang Wang, Wang Yingming, Li Tingting, Li Shenglong, Huang Jingjing, Wang Jianwei, Zhu Ju, Chen Dan, Wu Qingchen, Tao Kun, Pang Da, Jin Aishun", "evidence": [ { "database": "IEDB", "id": "2801", "url": "https://www.iedb.org/epitope/2801" }, { "database": "IEDB", "id": "54507", "url": "https://www.iedb.org/epitope/54507" }, { "database": "IEDB", "id": "71996", "url": "https://www.iedb.org/epitope/71996" }, { "database": "IEDB", "id": "1313269", "url": "https://www.iedb.org/epitope/1313269" }, { "database": "IEDB", "id": "1316287", "url": "https://www.iedb.org/epitope/1316287" }, { "database": "IEDB", "id": "1317060", "url": "https://www.iedb.org/epitope/1317060" }, { "database": "IEDB", "id": "1318219", "url": "https://www.iedb.org/epitope/1318219" }, { "database": "IEDB", "id": "1319328", "url": "https://www.iedb.org/epitope/1319328" }, { "database": "IEDB", "id": "1326409", "url": "https://www.iedb.org/epitope/1326409" }, { "database": "IEDB", "id": "1547648", "url": "https://www.iedb.org/epitope/1547648" } ], "reference": [ { "type": "PubMed", "id": "34222571", "url": "https://glygen.org/publication/PubMed/34222571" } ] }, { "title": "Identification of HLA-A2 restricted CD8+ T cell epitopes in SARS-CoV-2 structural proteins.", "journal": "Journal of leukocyte biology", "date": "2021-12", "authors": "Deng Jieping, Pan Junping, Qiu Minghui, Mao Lipeng, Wang Zhigang, Zhu Guodong, Gao Lijuan, Su Jun, Hu Yutian, Luo Oscar Junhong, Chen Guobing, Wang Pengcheng", "evidence": [ { "database": "IEDB", "id": "1597686", "url": "https://www.iedb.org/epitope/1597686" }, { "database": "IEDB", "id": "1597845", "url": "https://www.iedb.org/epitope/1597845" } ], "reference": [ { "type": "PubMed", "id": "34231935", "url": "https://glygen.org/publication/PubMed/34231935" } ] }, { "title": "A Peptide Vaccine Candidate Tailored to Individuals' Genetics Mimics the Multi-Targeted T Cell Immunity of COVID-19 Convalescent Subjects.", "journal": "Frontiers in genetics", "date": "2021", "authors": "Somogyi Eszter, Csiszovszki Zsolt, Moln\u00e1r Levente, L\u0151rincz Orsolya, T\u00f3th J\u00f3zsef, Pattijn Sofie, Schockaert Jana, Mazy Aur\u00e9lie, Mikl\u00f3s Istv\u00e1n, P\u00e1ntya Katalin, P\u00e1les P\u00e9ter, T\u0151ke Enik\u0151 R", "evidence": [ { "database": "IEDB", "id": "1316310", "url": "https://www.iedb.org/epitope/1316310" }, { "database": "IEDB", "id": "1333812", "url": "https://www.iedb.org/epitope/1333812" } ], "reference": [ { "type": "PubMed", "id": "34249101", "url": "https://glygen.org/publication/PubMed/34249101" } ] }, { "title": "Immunity against seasonal human coronavirus OC43 mitigates fatal deterioration of COVID-19.", "journal": "International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases", "date": "2021-08", "authors": "Yamaguchi Tomoyuki, Shinagawa Toshie, Kobata Hisanobu, Nakagawa Hidemitsu", "evidence": [ { "database": "IEDB", "id": "1397994", "url": "https://www.iedb.org/epitope/1397994" } ], "reference": [ { "type": "PubMed", "id": "34273512", "url": "https://glygen.org/publication/PubMed/34273512" } ] }, { "title": "Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine.", "journal": "Nature", "date": "2021-09", "authors": "Oberhardt Valerie, Luxenburger Hendrik, Kemming Janine, Schulien Isabel, Ciminski Kevin, Giese Sebastian, Csernalabics Benedikt, Lang-Meli Julia, Janowska Iga, Staniek Julian, Wild Katharina, Basho Kristi, Marinescu Mircea Stefan, Fuchs Jonas, Topfstedt Fernando, Janda Ales, Sogukpinar Oezlem, Hilger Hanna, Stete Katarina, Emmerich Florian, Bengsch Bertram, Waller Cornelius F, Rieg Siegbert, Sagar , Boettler Tobias, Zoldan Katharina, Kochs Georg, Schwemmle Martin, Rizzi Marta, Thimme Robert, Neumann-Haefelin Christoph, Hofmann Maike", "evidence": [ { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" }, { "database": "IEDB", "id": "1310623", "url": "https://www.iedb.org/epitope/1310623" }, { "database": "IEDB", "id": "1310865", "url": "https://www.iedb.org/epitope/1310865" }, { "database": "IEDB", "id": "1311170", "url": "https://www.iedb.org/epitope/1311170" }, { "database": "IEDB", "id": "1318829", "url": "https://www.iedb.org/epitope/1318829" }, { "database": "IEDB", "id": "1321049", "url": "https://www.iedb.org/epitope/1321049" }, { "database": "IEDB", "id": "1323461", "url": "https://www.iedb.org/epitope/1323461" } ], "reference": [ { "type": "PubMed", "id": "34320609", "url": "https://glygen.org/publication/PubMed/34320609" } ] }, { "title": "SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Martinez-Flores D, Zepeda-Cervantes J, Cruz-Resendiz A, Aguirre-Sampieri S, Sampieri A, Vaca L", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": 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"https://glygen.org/publication/PubMed/34329696" } ] }, { "title": "Direct Comparison of N-Glycans and Their Isomers Derived from Spike Glycoprotein 1 of MERS-CoV, SARS-CoV-1, and SARS-CoV-2.", "journal": "Journal of proteome research", "date": "2021-09-03", "authors": "Cho Byeong Gwan, Gautam Sakshi, Peng Wenjing, Huang Yifan, Goli Mona, Mechref Yehia", "evidence": [ { "database": "GlyConnect", "id": "2956", "url": "https://glyconnect.expasy.org/browser/proteins/2956" } ], "reference": [ { "type": "PubMed", "id": "34369795", "url": "https://glygen.org/publication/PubMed/34369795" } ] }, { "title": "Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein.", "journal": "The Journal of biological chemistry", "date": "2021-09", "authors": "Chaurasia Priyanka, Nguyen Thi H O, Rowntree Louise C, Juno Jennifer A, Wheatley Adam K, Kent Stephen J, Kedzierska Katherine, Rossjohn Jamie, Petersen Jan", "evidence": [ { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" } ], "reference": [ { "type": "PubMed", "id": "34384783", "url": "https://glygen.org/publication/PubMed/34384783" } ] }, { "title": "A glycan gate controls opening of the SARS-CoV-2 spike protein.", "journal": "Nature chemistry", "date": "2021-10", "authors": "Sztain Terra, Ahn Surl-Hee, Bogetti Anthony T, Casalino Lorenzo, Goldsmith Jory A, Seitz Evan, McCool Ryan S, Kearns Fiona L, Acosta-Reyes Francisco, Maji Suvrajit, Mashayekhi Ghoncheh, McCammon J Andrew, Ourmazd Abbas, Frank Joachim, McLellan Jason S, Chong Lillian T, Amaro Rommie E", "evidence": [ { "database": "PubMed", "id": "34413500", "url": "https://glygen.org/publication/PubMed/34413500" } ], "reference": [ { "type": "PubMed", "id": "34413500", "url": "https://glygen.org/publication/PubMed/34413500" } ] }, { "title": "Cross-reactive CD4+ T cells enhance SARS-CoV-2 immune responses upon infection and vaccination.", "journal": "Science (New York, N.Y.)", 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Determinants in SARS-CoV-2 RBD-Based Antigen.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Jiang Min, Zhang Gaiping, Liu Hongliang, Ding Peiyang, Liu Yunchao, Tian Yuanyuan, Wang Yanwei, Wang Aiping", "evidence": [ { "database": "IEDB", "id": "1597861", "url": "https://www.iedb.org/epitope/1597861" } ], "reference": [ { "type": "PubMed", "id": "34621266", "url": "https://glygen.org/publication/PubMed/34621266" } ] }, { "title": "Immunogenic T cell epitopes of SARS-CoV-2 are recognized by circulating memory and na\u00efve CD8 T cells of unexposed individuals.", "journal": "EBioMedicine", "date": "2021-10", "authors": "Quiros-Fernandez Isaac, Poorebrahim Mansour, Fakhr Elham, Cid-Arregui Angel", "evidence": [ { "database": "IEDB", "id": "1309137", "url": "https://www.iedb.org/epitope/1309137" }, { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" } ], "reference": [ { "type": "PubMed", "id": "34627082", "url": 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"Three Specific Potential Epitopes That Could Be Recognized by T Cells of Convalescent COVID-19 Patients Were Identified From Spike Protein.", "journal": "Frontiers in immunology", "date": "2022", "authors": "Zhang Yunwen, Yang Zhengrong, Tang Mingyuan, Li Hao, Tang Tian, Li Guilian, Zhong Yifan, Zhang Xiaomin, Wang Xiaohui, Wang Chuan", "evidence": [ { "database": "IEDB", "id": "1310259", "url": "https://www.iedb.org/epitope/1310259" }, { "database": "IEDB", "id": "1310306", "url": "https://www.iedb.org/epitope/1310306" }, { "database": "IEDB", "id": "1310360", "url": "https://www.iedb.org/epitope/1310360" }, { "database": "IEDB", "id": "1310487", "url": "https://www.iedb.org/epitope/1310487" }, { "database": "IEDB", "id": "1310649", "url": "https://www.iedb.org/epitope/1310649" }, { "database": "IEDB", "id": "1310787", "url": "https://www.iedb.org/epitope/1310787" }, { "database": "IEDB", "id": "1310863", "url": "https://www.iedb.org/epitope/1310863" } ], "reference": [ { "type": 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potential of progeny virions.", "journal": "Life sciences", "date": "2022-04-15", "authors": "Bhatt Anant Narayan, Kumar Abhishek, Rai Yogesh, Kumari Neeraj, Vedagiri Dhiviya, Harshan Krishnan H, Chinnadurai Vijayakumar, Chandna Sudhir", "evidence": [ { "database": "PubMed", "id": "35181310", "url": "https://glygen.org/publication/PubMed/35181310" } ], "reference": [ { "type": "PubMed", "id": "35181310", "url": "https://glygen.org/publication/PubMed/35181310" } ] }, { "title": "Limited Recognition of Highly Conserved Regions of SARS-CoV-2.", "journal": "Microbiology spectrum", "date": "2022-02-23", "authors": "Swaminathan Srividhya, Lineburg Katie E, Ambalathingal George R, Crooks Pauline, Grant Emma J, Mohan Sonali V, Raju Jyothy, Panikkar Archana, Le Texier Laetitia, Tong Zheng Wei Marcus, Chew Keng Yih, Neller Michelle A, Short Kirsty R, Gowda Harsha, Gras Stephanie, Khanna Rajiv, Smith Corey", "evidence": [ { "database": "IEDB", "id": "1075121", "url": 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targeting a conserved SARS-CoV-2 spike epitope are efficient serial killers.", "journal": "BioTechniques", "date": "2022-04", "authors": "Fathi Mohsen, Charley Lindsey, Cooper Laurence Jn, Varadarajan Navin, Meyer Daniel D", "evidence": [ { "database": "IEDB", "id": "1074952", "url": "https://www.iedb.org/epitope/1074952" } ], "reference": [ { "type": "PubMed", "id": "35297693", "url": "https://glygen.org/publication/PubMed/35297693" } ] }, { "title": "Establishment and recall of SARS-CoV-2 spike epitope-specific CD4+ T cell memory.", "journal": "Nature immunology", "date": "2022-05", "authors": "Wragg Kathleen M, Lee Wen Shi, Koutsakos Marios, Tan Hyon-Xhi, Amarasena Thakshila, Reynaldi Arnold, Gare Grace, Konstandopoulos Penny, Field Kirsty R, Esterbauer Robyn, Kent Helen E, Davenport Miles P, Wheatley Adam K, Kent Stephen J, Juno Jennifer A", "evidence": [ { "database": "IEDB", "id": "1310865", "url": "https://www.iedb.org/epitope/1310865" } ], "reference": [ { "type": "PubMed", 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Allison M, Crawford Jeremy Chase, Allen E Kaitlynn, Chou Ching-Heng, Mettelman Robert C, Allison Kim J, Lin Chun-Yang, Brice David C, Zhu Xun, Vegesana Kasi, Wu Gang, Trivedi Sanchit, Kottapalli Pratibha, Darnell Daniel, McNeely Suzanne, Olsen Scott R, Schultz-Cherry Stacey, Estepp Jeremie H, , McGargill Maureen A, Wolf Joshua, Thomas Paul G", "evidence": [ { "database": "IEDB", "id": "1220", "url": "https://www.iedb.org/epitope/1220" }, { "database": "IEDB", "id": "1075005", "url": "https://www.iedb.org/epitope/1075005" }, { "database": "IEDB", "id": "1309147", "url": "https://www.iedb.org/epitope/1309147" }, { "database": "IEDB", "id": "1310623", "url": "https://www.iedb.org/epitope/1310623" }, { "database": "IEDB", "id": "1310756", "url": "https://www.iedb.org/epitope/1310756" }, { "database": "IEDB", "id": "1313269", "url": "https://www.iedb.org/epitope/1313269" } ], "reference": [ { "type": "PubMed", "id": "35383307", "url": "https://glygen.org/publication/PubMed/35383307" } ] }, 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K, Hawman David W, Chu Helen Y, Hasenkrug Kim J, Fuller Deborah H, Matsen Iv Frederick A, Overbaugh Julie", "evidence": [ { "database": "IEDB", "id": "1966318", "url": "https://www.iedb.org/epitope/1966318" } ], "reference": [ { "type": "PubMed", "id": "35404959", "url": "https://glygen.org/publication/PubMed/35404959" } ] }, { "title": "Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.", "journal": "Communications biology", "date": "2022-04-11", "authors": "Hurlburt Nicholas K, Homad Leah J, Sinha Irika, Jennewein Madeleine F, MacCamy Anna J, Wan Yu-Hsin, Boonyaratanakornkit Jim, Sholukh Anton M, Jackson Abigail M, Zhou Panpan, Burton Dennis R, Andrabi Raiees, Ozorowski Gabriel, Ward Andrew B, Stamatatos Leonidas, Pancera Marie, McGuire Andrew T", "evidence": [ { "database": "IEDB", "id": "1972993", "url": "https://www.iedb.org/epitope/1972993" } ], "reference": [ { "type": "PubMed", "id": "35411021", "url": 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Tereza, Prochazka Jan, Guerrini Giuditta, Mehn Dora, Ciabattini Annalisa, Abolhassani Hassan, Jarrossay David, Uguccioni Mariagrazia, Medaglini Donata, Pan-Hammarstr\u00f6m Qiang, Calzolai Luigi, Fernandez Daniel, Baldanti Fausto, Franzetti-Pellanda Alessandra, Garzoni Christian, Sedlacek Radislav, Ruzek Daniel, Varani Luca, Cavalli Andrea, Barnes Christopher O, Robbiani Davide F", "evidence": [ { "database": "IEDB", "id": "1595221", "url": "https://www.iedb.org/epitope/1595221" } ], "reference": [ { "type": "PubMed", "id": "36701425", "url": "https://glygen.org/publication/PubMed/36701425" } ] }, { "title": "LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein.", "journal": "PLoS Biol.", "date": "2023", "authors": "Shilts Jarrod, Crozier Thomas W M, Teixeira-Silva Ana, Gabaev Ildar, Gerber Pehu\u00e9n Pereyra, Greenwood Edward J D, Watson Samuel James, Ortmann Brian M, Gawden-Bone Christian M, Pauzaite Tekle, Hoffmann Markus, Nathan James A, P\u00f6hlmann Stefan, Matheson Nicholas J, Lehner Paul J, Wright Gavin J", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "36735681", "url": "https://glygen.org/publication/PubMed/36735681" } ] }, { "title": "Transferrin Receptor Protein 1 Cooperates with mGluR2 To Mediate the Internalization of Rabies Virus and SARS-CoV-2.", "journal": "Journal of virology", "date": "2023-02-28", "authors": "Wang Xinxin, Wen Zhiyuan, Cao Huizhen, Luo Jie, Shuai Lei, Wang Chong, Ge Jinying, Wang Xijun, Bu Zhigao, Wang Jinliang", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "36779763", "url": "https://glygen.org/publication/PubMed/36779763" } ] }, { "title": "Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor (TCR) diversity.", "journal": "The Journal of biological chemistry", "date": "2023-02-16", "authors": "Wu Daichao, Efimov Grigory A, Bogolyubova Apollinariya V, Pierce Brian G, Mariuzza Roy A", "evidence": [ { "database": "IEDB", "id": "54725", "url": "https://www.iedb.org/epitope/54725" } ], "reference": [ { "type": "PubMed", "id": "36806685", "url": "https://glygen.org/publication/PubMed/36806685" } ] }, { "title": "Identification of Closed Linear Epitopes in S1-RBD and S2-HR1/2 of SARS-CoV-2 Spike Protein Able to Induce Neutralizing Abs.", "journal": "Vaccines", "date": "2023-01-28", "authors": "Watanabe Yoshihiro, Hosokawa Natsuko, Yoshida Misaki, Miura Tomoyuki, Kawano Mitsuhiro", "evidence": [ { "database": "IEDB", "id": "2223095", "url": "https://www.iedb.org/epitope/2223095" } ], "reference": [ { "type": "PubMed", "id": "36851165", "url": "https://glygen.org/publication/PubMed/36851165" } ] }, { "title": "The D405N Mutation in the Spike Protein of SARS-CoV-2 Omicron BA.5 Inhibits Spike/Integrins Interaction and Viral Infection of Human Lung Microvascular Endothelial Cells.", "journal": "Viruses", "date": "2023-01-24", "authors": "Bugatti Antonella, Filippini Federica, Messali Serena, Giovanetti Marta, Ravelli Cosetta, Zani Alberto, Ciccozzi Massimo, Caruso Arnaldo, Caccuri Francesca", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "36851546", "url": "https://glygen.org/publication/PubMed/36851546" } ] }, { "title": "A novel mAb broadly neutralizes SARS-CoV-2 VOCs in vitro and in vivo, including the Omicron variants.", "journal": "Journal of medical virology", "date": "2023-03", "authors": "Kan Qiuqi, Lin Xian, Li Tuofan, Ke Xianliang, Jian Xiaoqin, Hou Lidan, Zhang Wenyuan, Wan Zhimin, Xie Quan, Shao Hongxia, Ye Lilin, Ye Jianqiang, Qin Aijian, Zou Zhong, Chen Quanjiao", "evidence": [ { "database": "IEDB", "id": "1397122", "url": "https://www.iedb.org/epitope/1397122" } ], "reference": [ { "type": "PubMed", "id": 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Dcosta Belinda M, Landau Nathaniel R", "evidence": [ { "database": "IEDB", "id": "70066", "url": "https://www.iedb.org/epitope/70066" } ], "reference": [ { "type": "PubMed", "id": "37036004", "url": "https://glygen.org/publication/PubMed/37036004" } ] }, { "title": "Large libraries of single-chain trimer peptide-MHCs enable antigen-specific CD8+ T cell discovery and analysis.", "journal": "Communications biology", "date": "2023-05-16", "authors": "Chour William, Choi Jongchan, Xie Jingyi, Chaffee Mary E, Schmitt Thomas M, Finton Kathryn, DeLucia Diana C, Xu Alexander M, Su Yapeng, Chen Daniel G, Zhang Rongyu, Yuan Dan, Hong Sunga, Ng Alphonsus H C, Butler Jonah Z, Edmark Rick A, Jones Lesley C, Murray Kim M, Peng Songming, Li Guideng, Strong Roland K, Lee John K, Goldman Jason D, Greenberg Philip D, Heath James R", "evidence": [ { "database": "IEDB", "id": "37289", "url": "https://www.iedb.org/epitope/37289" }, { "database": "IEDB", "id": "54507", "url": 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"url": "https://www.iedb.org/epitope/1309147" } ], "reference": [ { "type": "PubMed", "id": "37390223", "url": "https://glygen.org/publication/PubMed/37390223" } ] }, { "title": "TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry.", "journal": "Cell", "date": "2023-08-03", "authors": "Baggen Jim, Jacquemyn Maarten, Persoons Leentje, Vanstreels Els, Pye Valerie E, Wrobel Antoni G, Calvaresi Valeria, Martin Stephen R, Roustan Chlo\u00eb, Cronin Nora B, Reading Eamonn, Thibaut Hendrik Jan, Vercruysse Thomas, Maes Piet, De Smet Frederik, Yee Angie, Nivitchanyong Toey, Roell Marina, Franco-Hernandez Natalia, Rhinn Herve, Mamchak Alusha Andre, Ah Young-Chapon Maxime, Brown Eric, Cherepanov Peter, Daelemans Dirk", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "reference": [ { "type": "PubMed", "id": "37421949", "url": "https://glygen.org/publication/PubMed/37421949" } ] }, { "title": "A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.", "journal": "Nature", "date": "2023-08", "authors": "Augusto Danillo G, Murdolo Lawton D, Chatzileontiadou Demetra S M, Sabatino Joseph J, Yusufali Tasneem, Peyser Noah D, Butcher Xochitl, Kizer Kerry, Guthrie Karoline, Murray Victoria W, Pae Vivian, Sarvadhavabhatla Sannidhi, Beltran Fiona, Gill Gurjot S, Lynch Kara L, Yun Cassandra, Maguire Colin T, Peluso Michael J, Hoh Rebecca, Henrich Timothy J, Deeks Steven G, Davidson Michelle, Lu Scott, Goldberg Sarah A, Kelly J Daniel, Martin Jeffrey N, Vierra-Green Cynthia A, Spellman Stephen R, Langton David J, Dewar-Oldis Michael J, Smith Corey, Barnard Peter J, Lee Sulggi, Marcus Gregory M, Olgin Jeffrey E, Pletcher Mark J, Maiers Martin, Gras Stephanie, Hollenbach Jill A", "evidence": [ { "database": "IEDB", "id": "7247", "url": "https://www.iedb.org/epitope/7247" }, { "database": "IEDB", "id": "1075005", "url": "https://www.iedb.org/epitope/1075005" } ], "reference": [ { "type": "PubMed", "id": "37468623", "url": "https://glygen.org/publication/PubMed/37468623" } ] }, { "title": "Identification and characterization of T-cell receptors with therapeutic potential showing conserved specificity against all SARS-CoV 2 strains.", "journal": "Immunobiology", "date": "2023-09", "authors": "Reimann Hannah, Moosmann Carolin, Schober Kilian, Lang Vanessa, Verhagen Johan, Zeun Julia, Mackensen Andreas, Kremer Anita N, V\u00f6lkl Simon, Aigner Michael", "evidence": [ { "database": "IEDB", "id": "1313194", "url": "https://www.iedb.org/epitope/1313194" }, { "database": "IEDB", "id": "1532692", "url": "https://www.iedb.org/epitope/1532692" } ], "reference": [ { "type": "PubMed", "id": "37541134", "url": "https://glygen.org/publication/PubMed/37541134" } ] }, { "title": "Phase I/II trial of a peptide-based COVID-19 T-cell activator in patients with B-cell deficiency.", "journal": "Nature communications", "date": "2023-08-18", "authors": "Heitmann Jonas S, Tandler Claudia, Marconato Maddalena, Nelde Annika, Habibzada Timorshah, Rittig Susanne M, Tegeler Christian M, Maringer Yacine, Jaeger Simon U, Denk Monika, Richter Marion, Oezbek Melek T, Wiesm\u00fcller Karl-Heinz, Bauer Jens, Rieth Jonas, Wacker Marcel, Schroeder Sarah M, Hoenisch Gravel Naomi, Scheid Jonas, M\u00e4rklin Melanie, Henrich Annika, Klimovich Boris, Clar Kim L, Lutz Martina, Holzmayer Samuel, H\u00f6rber Sebastian, Peter Andreas, Meisner Christoph, Fischer Imma, L\u00f6ffler Markus W, Peuker Caroline Anna, Habringer Stefan, Goetze Thorsten O, J\u00e4ger Elke, Rammensee Hans-Georg, Salih Helmut R, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310513", "url": "https://www.iedb.org/epitope/1310513" } ], "reference": [ { "type": "PubMed", "id": "37596280", "url": "https://glygen.org/publication/PubMed/37596280" } ] }, { "title": "Detection of Antibodies against Endemic and SARS-CoV-2 Coronaviruses with Short Peptide Epitopes.", "journal": "Vaccines", "date": "2023-08-23", "authors": "Szardenings Michael, Delaroque Nicolas, Kern Karolin, Ramirez-Caballero Lisbeth, Puder Marcus, Ehrentreich-F\u00f6rster Eva, Beige Joachim, Z\u00fcrner Sebastian, Popp Georg, Wolf Johannes, Borte Stephan", "evidence": [ { "database": "IEDB", "id": "1311839", "url": "https://www.iedb.org/epitope/1311839" }, { "database": "IEDB", "id": "1330147", "url": "https://www.iedb.org/epitope/1330147" }, { "database": "IEDB", "id": "1330292", "url": "https://www.iedb.org/epitope/1330292" } ], "reference": [ { "type": "PubMed", "id": "37766081", "url": "https://glygen.org/publication/PubMed/37766081" } ] }, { "title": "SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies.", "journal": "Scientific reports", "date": "2023-10-05", "authors": "Cioffi Victor Bolsanelli, de Castro-Amarante Maria Fernanda, Lulla Aleksei, Andreata-Santos Robert, Cruz Mario Costa, Moreno Ana 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], "pmid": "" }, { "name": "structural constituent of virion", "id": "GO:0039660", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0039660", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 12, "go_terms": [ { "name": "positive regulation of viral entry into host cell", "id": "GO:0046598", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0046598", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "symbiont entry into host cell", "id": "GO:0046718", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0046718", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "receptor-mediated virion attachment to host cell", "id": "GO:0046813", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0046813", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "membrane fusion", "id": "GO:0061025", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0061025", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "fusion of virus membrane with host plasma membrane", "id": "GO:0019064", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019064", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "virion attachment to host cell", "id": "GO:0019062", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019062", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "symbiont-mediated-mediated suppression of host tetherin activity", "id": "GO:0039587", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0039587", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "endocytosis involved in viral entry into host cell", "id": "GO:0075509", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0075509", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "fusion of virus membrane with host endosome membrane", "id": "GO:0039654", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0039654", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "entry receptor-mediated virion attachment to host cell", "id": "GO:0098670", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0098670", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "symbiont-mediated suppression of host innate immune response", "id": "GO:0052170", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0052170", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" }, { "name": "symbiont-mediated disruption of host tissue", "id": "GO:0141146", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0141146", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [ { "start_pos": 1074, "end_pos": 1076, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1098, "end_pos": 1100, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1134, "end_pos": 1136, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1158, "end_pos": 1160, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1173, "end_pos": 1175, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1194, "end_pos": 1196, "annotation": "n_glycosylation_sequon" }, { "start_pos": 122, "end_pos": 124, "annotation": "n_glycosylation_sequon" }, { "start_pos": 149, "end_pos": 151, "annotation": "n_glycosylation_sequon" }, { "start_pos": 165, "end_pos": 167, "annotation": "n_glycosylation_sequon" }, { "start_pos": 17, "end_pos": 19, "annotation": "n_glycosylation_sequon" }, { "start_pos": 234, "end_pos": 236, "annotation": "n_glycosylation_sequon" }, { "start_pos": 282, "end_pos": 284, "annotation": "n_glycosylation_sequon" }, { "start_pos": 331, "end_pos": 333, "annotation": "n_glycosylation_sequon" }, { "start_pos": 343, "end_pos": 345, "annotation": "n_glycosylation_sequon" }, { "start_pos": 603, "end_pos": 605, "annotation": "n_glycosylation_sequon" }, { "start_pos": 616, "end_pos": 618, "annotation": "n_glycosylation_sequon" }, { "start_pos": 61, "end_pos": 63, "annotation": "n_glycosylation_sequon" }, { "start_pos": 657, "end_pos": 659, "annotation": "n_glycosylation_sequon" }, { 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Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32363391, PubMed:32366695, PubMed:32929138). Approximately 40% of the protein surface is shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain (PubMed:32929138).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32929138", "url": "https://glygen.org/publication/PubMed/32929138" }, { "database": "PubMed", "id": "32155444", "url": "https://glygen.org/publication/PubMed/32155444" }, { "database": "PubMed", "id": "32366695", "url": "https://glygen.org/publication/PubMed/32366695" }, { "database": "PubMed", "id": "32075877", "url": "https://glygen.org/publication/PubMed/32075877" }, { "database": "PubMed", "id": "32363391", "url": "https://glygen.org/publication/PubMed/32363391" } ] }, { "annotation": "O-glycosylated by host GALNT1 at the end of S1. This could reduce the efficiency of S1/S2 cleavage.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34732583", "url": "https://glygen.org/publication/PubMed/34732583" } ] }, { "annotation": "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host furin or unknown proteases to yield the mature S1 and S2 proteins (PubMed:32155444, PubMed:32362314, PubMed:32703818, PubMed:34159616, PubMed:34561887). Processing between S2 and S2' occurs either by host CTSL in endosomes (PubMed:32221306, PubMed:33465165, PubMed:34159616), or by host TMPRSS2 at the cell surface (PubMed:32142651). Both cleavages are necessary for the protein to be fusion competent (PubMed:32703818, PubMed:34159616, PubMed:34561887). Cell surface activation allows the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). The polybasic furin cleavage site is absent in SARS-CoV S (PubMed:32155444, PubMed:32362314, PubMed:33465165). It increases the dependence on TMPRSS2 expression by SARS-CoV-2 (PubMed:33465165). D614G substitution would enhance furin cleavage at the S1/S2 junction (PubMed:33417835).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "32155444", "url": "https://glygen.org/publication/PubMed/32155444" }, { "database": "PubMed", "id": "32142651", "url": "https://glygen.org/publication/PubMed/32142651" }, { "database": "PubMed", "id": "32362314", "url": "https://glygen.org/publication/PubMed/32362314" }, { "database": "PubMed", "id": "33465165", "url": "https://glygen.org/publication/PubMed/33465165" }, { "database": "PubMed", "id": "34561887", "url": "https://glygen.org/publication/PubMed/34561887" }, { "database": "PubMed", "id": "32703818", "url": "https://glygen.org/publication/PubMed/32703818" }, { "database": "PubMed", "id": "33417835", "url": "https://glygen.org/publication/PubMed/33417835" }, { "database": "PubMed", "id": "34159616", "url": "https://glygen.org/publication/PubMed/34159616" }, { "database": "PubMed", "id": "32221306", "url": "https://glygen.org/publication/PubMed/32221306" } ] }, { "annotation": "The cytoplasmic Cys-rich domain is palmitoylated. Palmitoylated spike proteins drive the formation of localized ordered cholesterol and sphingo-lipid-rich lipid nanodomains in the early Golgi, where viral budding occurs.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC2", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "database": "PubMed", "id": "34599882", "url": "https://glygen.org/publication/PubMed/34599882" } ] } ], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "structures": [], "lectin_list": [ { "lectin_class": "Coronavirus spike protein", "evidence": [ { "id": "35737812", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35737812" }, { "id": "10.1126/science.abm3125", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1126/science.abm3125" } ] } ], "domain_list": [ { "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "id": "32132184", "database": "PubMed", 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"Asn122,Asn149,Asn234,Asn282,Asn61,Asn74,Asn165,Asn17,Thr124,Ser151,Thr63,Ser71,Thr73,Thr76,Ser94,Thr95,Thr114,Thr167,Thr236,Asn125,Asn280,Ser254,Asn164,Asn137,Asn148,Asn188,Asn30,Asn121" }, { "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "id": "34504087", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34504087" } ], "ann_type": "Motif_Annotation", "uniprotkb_annotation": "Binding to host endocytosis trafficking protein SNX27", "eco_id": "ECO_0000269", "start_pos": 1237, "end_pos": 1241, "start_aa": "Met", "end_aa": "Cys", "glycosite_overlap": "" }, { "evidence": [ { "id": "P0DTC2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC2" }, { "id": "34504087", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34504087" } ], "ann_type": "Motif_Annotation", "uniprotkb_annotation": "Binding to host plasma membrane localising/FERM domain proteins", "eco_id": 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"end_pos": 1273, "start_aa": "Lys", "end_aa": "Thr", "glycosite_overlap": "" } ], "binding_sites": [], "synthesized_glycans": [], "enzyme_annotation": [], "cluster_types": [ { "name": "homologset.uniref", "label": "UniRef Homologs" } ], "sequence_features": { "n_linked_sites": [ 17, 30, 61, 74, 121, 122, 125, 137, 148, 149, 164, 165, 188, 234, 280, 282, 331, 334, 343, 354, 370, 460, 487, 603, 616, 657, 658, 679, 703, 709, 710, 717, 801, 928, 1074, 1098, 1125, 1134, 1158, 1173, 1194 ], "o_linked_sites": [ 63, 71, 73, 76, 94, 95, 114, 124, 151, 167, 236, 254, 315, 323, 325, 333, 345, 376, 415, 417, 478, 489, 505, 523, 618, 676, 678, 803, 1076, 1077, 1097, 1100 ], "snv_sites": [], "glycation_sites": [], "phosphorylation_sites": [], "sequon_annotation_sites": [ { "start_pos": 1074, "end_pos": 1076 }, { "start_pos": 1098, "end_pos": 1100 }, { "start_pos": 1134, "end_pos": 1136 }, { "start_pos": 1158, "end_pos": 1160 }, { "start_pos": 1173, "end_pos": 1175 }, { "start_pos": 1194, "end_pos": 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"uniprot_ac": "P0DTC3", "uniprot_id": "AP3A_SARS2", "mass": { "chemical_mass": 31123.0, "monoisotopic_mass": 31123.0 }, "refseq": { "ac": "YP_009724391", "name": "ORF3a protein", "summary": "", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724391" }, "gene_names": [ { "name": "3a", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ] } ], "protein_names": [ { "name": "ORF3a protein", "type": "recommended", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] }, { "name": "Accessory protein 3a", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] }, { "name": "ORF3a protein", "type": "synonym", "evidence": [ { "id": "YP_009724391", "database": "RefSeq", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724391" } ] }, { "name": "ORF3a", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] }, { "name": "Protein 3a", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] }, { "name": "Protein U274", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] }, { "name": "Protein X1", "type": "synonym", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#names_and_taxonomy" } ] } ], "function": [ { "annotation": "Plays a role in viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporins) localized at endosomes and lysosomes, that may induce deacidification of lysosomes, allowing safe egress of virions via lysosomal trafficking (PubMed:33157038, PubMed:33422265, PubMed:34158638). Also blocks autolysosome formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes (PubMed:33422265). This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265). Induces host RETREG1/FAM134B-dependent reticulophagy by interacting with host HMGB1 and enhancing the association between HMGB1 and host BECN1 (PubMed:35239449). This induces endoplasmic reticulum stress and inflammatory responses and facilitates viral infection (PubMed:35239449).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3#function" }, { "database": "PubMed", "id": "33157038", "url": "https://glygen.org/publication/PubMed/33157038" }, { "database": "PubMed", "id": "35239449", "url": "https://glygen.org/publication/PubMed/35239449" }, { "database": "PubMed", "id": "33422265", "url": "https://glygen.org/publication/PubMed/33422265" }, { "database": "PubMed", "id": "34158638", "url": "https://glygen.org/publication/PubMed/34158638" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe 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"sequence_org": "MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASL", "sequence_mut": "", "comment": "Partial loss of Ca(2+) and NMDG(+) permeability. Increased localization at host plasma membrane.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" }, { "database": "PubMed", "id": "34158638", "url": "https://glygen.org/publication/PubMed/34158638" } ] }, { "start_pos": 57, "end_pos": 57, "sequence_org": "Q", "sequence_mut": "H", "comment": "No effect on ion permeability.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" }, { "database": "PubMed", "id": "34158638", "url": "https://glygen.org/publication/PubMed/34158638" } ] }, { "start_pos": 57, "end_pos": 58, "sequence_org": "QS", "sequence_mut": "EL", "comment": "Partial loss of Ca(2+) and NMDG(+) permeability.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" }, { "database": "PubMed", "id": "34158638", "url": "https://glygen.org/publication/PubMed/34158638" } ] } ], "expression_tissue": [], 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] }, { "id": "P0DTC3", "url": "https://viral.glycomics.ku.dk/viewer/?uniprot=P0DTC3", "database": "Viral Glycome", "categories": [ "Organism-specific" ] } ], "sequence": { "sequence": "MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL", "length": 275, "header": "sp|P0DTC3-1|AP3A_SARS2 Isoform 1 of ORF3a protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC3-1" }, "isoforms": [ { "isoform_ac": "P0DTC3-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC3/entry#P0DTC3-1", "sequence": { "sequence": 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"https://www.uniprot.org/uniprotkb/P0DTC3#ptm_processing" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_pos": 34, "start_aa": "Thr", "end_pos": 34, "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr34", "evidence": [ { "id": "P0DTC3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC3#ptm_processing" } ] } ], "phosphorylation": [], "glycation": [], "keywords": [ "glycoprotein", "glycoprotein_predicted" ], "publication": [ { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1074846", "url": "https://www.iedb.org/epitope/1074846" }, { "database": "IEDB", "id": "1087430", "url": "https://www.iedb.org/epitope/1087430" }, { "database": "IEDB", "id": "1310411", "url": "https://www.iedb.org/epitope/1310411" }, { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "Unbiased Screens Show CD8+ T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein.", "journal": "Immunity", "date": "2020-11-17", "authors": "Ferretti Andrew P, Kula Tomasz, Wang Yifan, Nguyen Dalena M V, Weinheimer Adam, Dunlap Garrett S, Xu Qikai, Nabilsi Nancy, Perullo Candace R, Cristofaro Alexander W, Whitton Holly J, Virbasius Amy, Olivier Kenneth J, Buckner Lyndsey R, Alistar Angela T, Whitman Eric D, Bertino Sarah A, Chattopadhyay Shrikanta, MacBeath Gavin", "evidence": [ { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" }, { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" } ], "reference": [ { "type": "PubMed", "id": "33128877", "url": "https://glygen.org/publication/PubMed/33128877" } ] }, { "title": "\u03b2-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway.", "journal": "Cell", "date": "2020-12-10", "authors": "Ghosh Sourish, Dellibovi-Ragheb Teegan A, Kerviel Adeline, Pak Eowyn, Qiu Qi, Fisher Matthew, Takvorian Peter M, Bleck Christopher, Hsu Victor W, Fehr Anthony R, Perlman Stanley, Achar Sooraj R, Straus Marco R, Whittaker Gary R, de Haan Cornelis A M, Kehrl John, Altan-Bonnet Gr\u00e9goire, Altan-Bonnet Nihal", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ], "reference": [ { "type": "PubMed", "id": "33157038", "url": "https://glygen.org/publication/PubMed/33157038" } ] }, { "title": "Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells.", "journal": "Nature medicine", "date": "2021-01", "authors": "Schulien Isabel, Kemming Janine, Oberhardt Valerie, Wild Katharina, Seidel Lea M, Killmer Saskia, Sagar , Daul Franziska, Salvat Lago Marilyn, Decker Annegrit, Luxenburger Hendrik, Binder Benedikt, Bettinger Dominik, Sogukpinar Oezlem, Rieg Siegbert, Panning Marcus, Huzly Daniela, Schwemmle Martin, Kochs Georg, Waller Cornelius F, Nieters Alexandra, Duerschmied Daniel, Emmerich Florian, Mei Henrik E, Schulz Axel Ronald, Llewellyn-Lacey Sian, Price David A, Boettler Tobias, Bengsch Bertram, Thimme Robert, Hofmann Maike, Neumann-Haefelin Christoph", "evidence": [ { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" }, { "database": "IEDB", "id": "1311604", "url": "https://www.iedb.org/epitope/1311604" } ], "reference": [ { "type": "PubMed", "id": "33184509", "url": "https://glygen.org/publication/PubMed/33184509" } ] }, { "title": "ORF3a of the COVID-19 virus SARS-CoV-2 blocks HOPS complex-mediated assembly of the SNARE complex required for autolysosome formation.", "journal": "Developmental cell", "date": "2021", "authors": "Miao G, Zhao H, Li Y, Ji M, Chen Y, Shi Y, Bi Y, Wang P, Zhang H", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ], "reference": [ { "type": "PubMed", "id": "33422265", "url": "https://glygen.org/publication/PubMed/33422265" } ] }, { "title": "SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals.", "journal": "The Journal of clinical investigation", "date": "2021-03-01", "authors": "Kared Hassen, Redd Andrew D, Bloch Evan M, Bonny Tania S, Sumatoh Hermi, Kairi Faris, Carbajo Daniel, Abel Brian, Newell Evan W, Bettinotti Maria P, Benner Sarah E, Patel Eshan U, Littlefield Kirsten, Laeyendecker Oliver, Shoham Shmuel, Sullivan David, Casadevall Arturo, Pekosz Andrew, Nardin Alessandra, Fehlings Michael, Tobian Aaron Ar, Quinn Thomas C", "evidence": [ { "database": "IEDB", "id": "1074846", "url": "https://www.iedb.org/epitope/1074846" }, { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" }, { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" }, { "database": "IEDB", "id": "1311604", "url": "https://www.iedb.org/epitope/1311604" }, { "database": "IEDB", "id": "1313530", "url": "https://www.iedb.org/epitope/1313530" } ], "reference": [ { "type": "PubMed", "id": "33427749", "url": "https://glygen.org/publication/PubMed/33427749" } ] }, { "title": "SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.", "journal": "Science immunology", "date": "2021-04-14", "authors": "Saini Sunil Kumar, Hersby Ditte Stampe, Tamhane Tripti, Povlsen Helle Rus, Amaya Hernandez Susana Patricia, Nielsen Morten, Gang Anne Ortved, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "1074846", "url": "https://www.iedb.org/epitope/1074846" }, { "database": "IEDB", "id": "1087430", "url": "https://www.iedb.org/epitope/1087430" }, { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1310278", "url": "https://www.iedb.org/epitope/1310278" }, { "database": "IEDB", "id": "1310408", "url": "https://www.iedb.org/epitope/1310408" }, { 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"1333888", "url": "https://www.iedb.org/epitope/1333888" }, { "database": "IEDB", "id": "1333994", "url": "https://www.iedb.org/epitope/1333994" }, { "database": "IEDB", "id": "1334275", "url": "https://www.iedb.org/epitope/1334275" }, { "database": "IEDB", "id": "1334349", "url": "https://www.iedb.org/epitope/1334349" } ], "reference": [ { "type": "PubMed", "id": "33853928", "url": "https://glygen.org/publication/PubMed/33853928" } ] }, { "title": "Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features.", "journal": "Nature communications", "date": "2021-05-10", "authors": "Gangaev Anastasia, Ketelaars Steven L C, Isaeva Olga I, Patiwael Sanne, Dopler Anna, Hoefakker Kelly, De Biasi Sara, Gibellini Lara, Mussini Cristina, Guaraldi Giovanni, Girardis Massimo, Ormeno Cami M P Talavera, Hekking Paul J M, Lardy Neubury M, Toebes Mireille, Balderas Robert, Schumacher Ton N, Ovaa Huib, Cossarizza Andrea, Kvistborg Pia", "evidence": [ { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" } ], "reference": [ { "type": "PubMed", "id": "33972535", "url": "https://glygen.org/publication/PubMed/33972535" } ] }, { "title": "Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs.", "journal": "Nature structural & molecular biology", "date": "2021", "authors": "Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ], "reference": [ { "type": "PubMed", "id": "34158638", "url": "https://glygen.org/publication/PubMed/34158638" } ] }, { "title": "Profiling CD8+ T\u00a0cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.", "journal": "Cell reports", "date": "2021-09-14", "authors": "Zhang Hang, Deng Shasha, Ren Liting, Zheng Peiyi, Hu Xiaowen, Jin Tengchuan, Tan Xu", "evidence": [ { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" }, { "database": "IEDB", "id": "1313129", "url": "https://www.iedb.org/epitope/1313129" } ], "reference": [ { "type": "PubMed", "id": "34506741", "url": "https://glygen.org/publication/PubMed/34506741" } ] }, { "title": "Immunogenic T cell epitopes of SARS-CoV-2 are recognized by circulating memory and na\u00efve CD8 T cells of unexposed individuals.", "journal": "EBioMedicine", "date": "2021-10", "authors": "Quiros-Fernandez Isaac, Poorebrahim Mansour, Fakhr Elham, Cid-Arregui Angel", "evidence": [ { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" } ], "reference": [ { "type": "PubMed", "id": "34627082", "url": "https://glygen.org/publication/PubMed/34627082" } ] }, { "title": "The impact of viral mutations on recognition by SARS-CoV-2 specific T\u00a0cells.", "journal": "iScience", "date": "2021-11-19", "authors": "de Silva Thushan I, Liu Guihai, Lindsey Benjamin B, Dong Danning, Moore Shona C, Hsu Nienyun Sharon, Shah Dhruv, Wellington Dannielle, Mentzer Alexander J, Angyal Adrienn, Brown Rebecca, Parker Matthew D, Ying Zixi, Yao Xuan, Turtle Lance, Dunachie Susanna, , Maini Mala K, Ogg Graham, Knight Julian C, , Peng Yanchun, Rowland-Jones Sarah L, Dong Tao", "evidence": [ { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" } ], "reference": [ { "type": "PubMed", "id": "34729465", "url": "https://glygen.org/publication/PubMed/34729465" } ] }, { "title": "Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2.", "journal": "Science immunology", "date": "2022-01-21", "authors": "Francis Joshua M, Leistritz-Edwards Del, Dunn Augustine, Tarr Christina, Lehman Jesse, Dempsey Conor, Hamel Andrew, Rayon Violeta, Liu Gang, Wang Yuntong, Wille Marcos, Durkin Melissa, Hadley Kane, Sheena Aswathy, Roscoe Benjamin, Ng Mark, Rockwell Graham, Manto Margaret, Gienger Elizabeth, Nickerson Joshua, , Moarefi Amir, Noble Michael, Malia Thomas, Bardwell Philip D, Gordon William, Swain Joanna, Skoberne Mojca, Sauer Karsten, Harris Tim, Goldrath Ananda W, Shalek Alex K, Coyle Anthony J, Benoist Christophe, Pregibon Daniel C", "evidence": [ { "database": "IEDB", "id": "1074846", "url": "https://www.iedb.org/epitope/1074846" }, { "database": "IEDB", "id": "1074931", "url": "https://www.iedb.org/epitope/1074931" }, { "database": "IEDB", "id": "1087430", "url": "https://www.iedb.org/epitope/1087430" }, { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" }, { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" }, { "database": "IEDB", "id": "1311604", "url": "https://www.iedb.org/epitope/1311604" }, { "database": "IEDB", "id": "1318163", "url": "https://www.iedb.org/epitope/1318163" }, { "database": 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"id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1310934", "url": "https://www.iedb.org/epitope/1310934" }, { "database": "IEDB", "id": "1311180", "url": "https://www.iedb.org/epitope/1311180" } ], "reference": [ { "type": "PubMed", "id": "34968416", "url": "https://glygen.org/publication/PubMed/34968416" } ] }, { "title": "Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair.", "journal": "Open biology", "date": "2022-02", "authors": "de Castro Mateus V, Santos Keity S, Apostolico Juliana S, Fernandes Edgar R, Almeida Rafael R, Levin Gabriel, Magawa Jhosiene Y, Nunes Jo\u00e3o Paulo S, Bruni Mirian, Yamamoto Marcio M, Lima Ariane C, Silva Monize V R, Matos Larissa R B, Coria Vivian R, Castelli Erick C, Scliar Marilia O, Kuramoto Andreia, Bruno Fernanda R, Jacintho Lucas C, Nunes Kelly, Wang Jaqueline Y T, Coelho Veronica P, Neto Miguel Mitne, Maciel Rui M B, Naslavsky Michel S, Passos-Bueno Maria Rita, Boscardin Silvia B, Rosa Daniela S, Kalil Jorge, Zatz Mayana, Cunha-Neto Edecio", "evidence": [ { "database": "IEDB", "id": "1310789", "url": "https://www.iedb.org/epitope/1310789" } ], "reference": [ { "type": "PubMed", "id": "35104433", "url": "https://glygen.org/publication/PubMed/35104433" } ] }, { "title": "SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion.", "journal": "FEBS J.", "date": "2022", "authors": "Quaglia Federica, Salladini Edoardo, Carraro Marco, Minervini Giovanni, Tosatto Silvio C E, Le Mercier Philippe", "evidence": [ { "database": "UniProtKB", "id": "P0DTC3", "url": "https://www.uniprot.org/uniprotkb/P0DTC3" } ], "reference": [ { "type": "PubMed", "id": "35108439", "url": "https://glygen.org/publication/PubMed/35108439" } ] }, { "title": "SARS-CoV-2-specific T cells generated for adoptive immunotherapy are capable of recognizing multiple SARS-CoV-2 variants.", "journal": "PLoS pathogens", "date": "2022-02", "authors": "Panikkar Archana, Lineburg Katie E, Raju Jyothy, Chew Keng Yih, Ambalathingal George R, Rehan Sweera, Swaminathan Srividhya, Crooks Pauline, Le Texier Laetitia, Beagley Leone, Best Shannon, Solomon Matthew, Matthews Katherine K, Srihari Sriganesh, Neller Michelle A, Short Kirsty R, Khanna Rajiv, Smith Corey", "evidence": [ { "database": "IEDB", "id": "1309115", "url": "https://www.iedb.org/epitope/1309115" }, { "database": "IEDB", "id": "1327990", "url": "https://www.iedb.org/epitope/1327990" } ], "reference": [ { "type": "PubMed", "id": "35157735", "url": "https://glygen.org/publication/PubMed/35157735" } ] }, { "title": "Limited Recognition of Highly Conserved Regions of SARS-CoV-2.", "journal": "Microbiology spectrum", "date": "2022-02-23", "authors": "Swaminathan Srividhya, Lineburg Katie E, Ambalathingal George R, Crooks Pauline, Grant Emma J, Mohan Sonali V, Raju Jyothy, Panikkar Archana, Le Texier Laetitia, Tong Zheng Wei Marcus, Chew Keng Yih, Neller Michelle A, 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identifies immunogenic T cell epitopes.", "journal": "Genome medicine", "date": "2020-08-13", "authors": "Poran Asaf, Harjanto Dewi, Malloy Matthew, Arieta Christina M, Rothenberg Daniel A, Lenkala Divya, van Buuren Marit M, Addona Terri A, Rooney Michael S, Srinivasan Lakshmi, Gaynor Richard B", "evidence": [ { "database": "IEDB", "id": "1125058", "url": "https://www.iedb.org/epitope/1125058" } ], "reference": [ { "type": "PubMed", "id": "32791978", "url": "https://glygen.org/publication/PubMed/32791978" } ] }, { "title": "Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis.", "journal": "Microbes and infection", "date": "2020", "authors": "De Maio F, Lo Cascio E, Babini G, Sali M, Della Longa S, Tilocca B, Roncada P, Arcovito A, Sanguinetti M, Scambia G, Urbani A", "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "reference": [ { "type": "PubMed", "id": "32891874", "url": "https://glygen.org/publication/PubMed/32891874" } ] }, { "title": "SARS-CoV-2 envelope protein topology in eukaryotic membranes.", "journal": "Open Biol.", "date": "2020", "authors": "Duart Gerard, Garc\u00eda-Murria M\u00aa Jes\u00fas, Grau Brayan, Acosta-C\u00e1ceres Jos\u00e9 M, Mart\u00ednez-Gil Luis, Mingarro Ismael", "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "reference": [ { "type": "PubMed", "id": "32898469", "url": "https://glygen.org/publication/PubMed/32898469" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310429", "url": "https://www.iedb.org/epitope/1310429" }, { "database": "IEDB", "id": "1310430", "url": "https://www.iedb.org/epitope/1310430" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.", "journal": "Nat. Struct. Mol. Biol.", "date": "2020", "authors": "Mandala Venkata S, McKay Matthew J, Shcherbakov Alexander A, Dregni Aurelio J, Kolocouris Antonios, Hong Mei", "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "reference": [ { "type": "PubMed", "id": "33177698", "url": "https://glygen.org/publication/PubMed/33177698" } ] }, { "title": "The SARS-CoV-2 envelope and membrane proteins modulate maturation and retention of the spike protein, allowing assembly of virus-like particles.", "journal": "The Journal of biological chemistry", "date": "2021", "authors": "Boson Bertrand, Legros Vincent, Zhou Bingjie, Siret Eglantine, Mathieu Cyrille, Cosset Fran\u00e7ois-Lo\u00efc, Lavillette Dimitri, Denolly Sol\u00e8ne", "evidence": [ { "database": "UniProtKB", "id": "P0DTC4", "url": "https://www.uniprot.org/uniprotkb/P0DTC4" } ], "reference": [ { "type": "PubMed", "id": "33229438", "url": "https://glygen.org/publication/PubMed/33229438" } ] }, { "title": "SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.", "journal": "Science immunology", "date": "2021-04-14", "authors": "Saini Sunil Kumar, Hersby Ditte Stampe, Tamhane Tripti, Povlsen Helle Rus, Amaya Hernandez Susana Patricia, Nielsen Morten, Gang Anne Ortved, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "1075128", "url": "https://www.iedb.org/epitope/1075128" }, { "database": "IEDB", "id": "1310626", "url": "https://www.iedb.org/epitope/1310626" } ], "reference": [ { "type": "PubMed", "id": "33853928", "url": "https://glygen.org/publication/PubMed/33853928" } ] }, { "title": "Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2021-06-01", "authors": "Prakash Swayam, Srivastava Ruchi, Coulon Pierre-Gregoire, Dhanushkodi Nisha R, Chentoufi Aziz A, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Buchmeier Michael J, Bouziane Mohammed, Nesburn Anthony B, Kuppermann Baruch D, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "16501", "url": "https://www.iedb.org/epitope/16501" }, { "database": "IEDB", "id": "16503", "url": "https://www.iedb.org/epitope/16503" }, { "database": "IEDB", "id": "16762", "url": "https://www.iedb.org/epitope/16762" }, { "database": "IEDB", "id": "16763", "url": "https://www.iedb.org/epitope/16763" } ], "reference": [ { "type": "PubMed", "id": "33911008", "url": "https://glygen.org/publication/PubMed/33911008" } ] }, { "title": "Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics.", "journal": "Cell reports", "date": "2021-06-29", "authors": "Nagler Adi, Kalaora Shelly, Barbolin Chaya, Gangaev Anastasia, Ketelaars Steven L C, Alon Michal, Pai Joy, Benedek Gil, Yahalom-Ronen Yfat, Erez Noam, Greenberg Polina, Yagel Gal, Peri Aviyah, Levin Yishai, Satpathy Ansuman T, Bar-Haim Erez, Paran Nir, Kvistborg Pia, Samuels Yardena", "evidence": [ { "database": "IEDB", "id": "1596831", "url": "https://www.iedb.org/epitope/1596831" } ], "reference": [ { "type": "PubMed", "id": "34166618", "url": "https://glygen.org/publication/PubMed/34166618" } ] }, { "title": "Identification of HLA-A2 restricted CD8+ T cell epitopes in SARS-CoV-2 structural proteins.", "journal": "Journal of leukocyte biology", "date": "2021-12", "authors": "Deng Jieping, Pan Junping, Qiu Minghui, Mao Lipeng, Wang Zhigang, Zhu Guodong, Gao Lijuan, Su Jun, Hu Yutian, Luo Oscar Junhong, Chen Guobing, Wang Pengcheng", "evidence": [ { "database": "IEDB", "id": "16762", "url": "https://www.iedb.org/epitope/16762" }, { "database": "IEDB", "id": "62214", "url": "https://www.iedb.org/epitope/62214" } ], "reference": [ { "type": "PubMed", "id": "34231935", "url": 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van Buuren Marit M, Addona Terri A, Rooney Michael S, Srinivasan Lakshmi, Gaynor Richard B", "evidence": [ { "database": "IEDB", "id": "1125059", "url": "https://www.iedb.org/epitope/1125059" } ], "reference": [ { "type": "PubMed", "id": "32791978", "url": "https://glygen.org/publication/PubMed/32791978" } ] }, { "title": "Suboptimal SARS-CoV-2-specific CD8+ T cell response associated with the prominent HLA-A*02:01 phenotype.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2020-09-29", "authors": "Habel Jennifer R, Nguyen Thi H O, van de Sandt Carolien E, Juno Jennifer A, Chaurasia Priyanka, Wragg Kathleen, Koutsakos Marios, Hensen Luca, Jia Xiaoxiao, Chua Brendon, Zhang Wuji, Tan Hyon-Xhi, Flanagan Katie L, Doolan Denise L, Torresi Joseph, Chen Weisan, Wakim Linda M, Cheng Allen C, Doherty Peter C, Petersen Jan, Rossjohn Jamie, Wheatley Adam K, Kent Stephen J, Rowntree Louise C, Kedzierska Katherine", "evidence": [ { "database": "IEDB", "id": "72759", "url": "https://www.iedb.org/epitope/72759" }, { "database": "IEDB", "id": "1125059", "url": "https://www.iedb.org/epitope/1125059" }, { "database": "IEDB", "id": "1309124", "url": "https://www.iedb.org/epitope/1309124" } ], "reference": [ { "type": "PubMed", "id": "32913053", "url": "https://glygen.org/publication/PubMed/32913053" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1075044", "url": "https://www.iedb.org/epitope/1075044" }, { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" }, { "database": "IEDB", "id": "1310684", "url": "https://www.iedb.org/epitope/1310684" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "Unbiased Screens Show CD8+ T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein.", "journal": "Immunity", "date": "2020-11-17", "authors": "Ferretti Andrew P, Kula Tomasz, Wang Yifan, Nguyen Dalena M V, Weinheimer Adam, Dunlap Garrett S, Xu Qikai, Nabilsi Nancy, Perullo Candace R, Cristofaro Alexander W, Whitton Holly J, Virbasius Amy, Olivier Kenneth J, Buckner Lyndsey R, Alistar Angela T, Whitman Eric D, Bertino Sarah A, Chattopadhyay Shrikanta, MacBeath Gavin", "evidence": [ { "database": "IEDB", "id": "5149", "url": "https://www.iedb.org/epitope/5149" }, { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" } ], "reference": [ { "type": "PubMed", "id": "33128877", "url": "https://glygen.org/publication/PubMed/33128877" } ] }, { "title": "The SARS-CoV-2 envelope and membrane proteins modulate maturation and retention of the spike protein, allowing assembly of virus-like particles.", "journal": "The Journal of biological chemistry", "date": "2021", "authors": "Boson Bertrand, Legros Vincent, Zhou Bingjie, Siret Eglantine, Mathieu Cyrille, Cosset Fran\u00e7ois-Lo\u00efc, Lavillette Dimitri, Denolly Sol\u00e8ne", "evidence": [ { "database": "UniProtKB", "id": "P0DTC5", "url": 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Swayam, Srivastava Ruchi, Coulon Pierre-Gregoire, Dhanushkodi Nisha R, Chentoufi Aziz A, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Buchmeier Michael J, Bouziane Mohammed, Nesburn Anthony B, Kuppermann Baruch D, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" }, { "database": "IEDB", "id": "1330469", "url": "https://www.iedb.org/epitope/1330469" }, { "database": "IEDB", "id": "1332347", "url": "https://www.iedb.org/epitope/1332347" } ], "reference": [ { "type": "PubMed", "id": "33911008", "url": "https://glygen.org/publication/PubMed/33911008" } ] }, { "title": "Identification and characterization of a SARS-CoV-2 specific CD8+ T cell response with immunodominant features.", "journal": "Nature communications", "date": "2021-05-10", "authors": "Gangaev Anastasia, Ketelaars Steven L C, Isaeva Olga I, Patiwael Sanne, Dopler Anna, Hoefakker Kelly, De Biasi Sara, Gibellini Lara, 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"url": "https://glygen.org/publication/PubMed/34814158" } ] }, { "title": "Recruitment of highly cytotoxic CD8+ T\u00a0cell receptors in mild SARS-CoV-2 infection.", "journal": "Cell reports", "date": "2022-01-11", "authors": "Wagner Karolin I, Mateyka Laura M, Jarosch Sebastian, Grass Vincent, Weber Simone, Schober Kilian, Hammel Monika, Burrell Teresa, Kalali Behnam, Poppert Holger, Beyer Henriette, Schambeck Sophia, Holdenrieder Stefan, Str\u00f6tges-Achatz Andrea, Haselmann Verena, Neumaier Michael, Erber Johanna, Priller Alina, Yazici Sarah, Roggendorf Hedwig, Odendahl Marcus, Tonn Torsten, Dick Andrea, Witter Klaus, Mijo\u010devi\u0107 Hrvoje, Protzer Ulrike, Knolle Percy A, Pichlmair Andreas, Crowell Claudia S, Gerhard Markus, D'Ippolito Elvira, Busch Dirk H", "evidence": [ { "database": "IEDB", "id": "1075044", "url": "https://www.iedb.org/epitope/1075044" } ], "reference": [ { "type": "PubMed", "id": "34968416", "url": "https://glygen.org/publication/PubMed/34968416" } ] }, { 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"https://glygen.org/publication/PubMed/35104433" } ] }, { "title": "SARS-CoV-2-specific T cells generated for adoptive immunotherapy are capable of recognizing multiple SARS-CoV-2 variants.", "journal": "PLoS pathogens", "date": "2022-02", "authors": "Panikkar Archana, Lineburg Katie E, Raju Jyothy, Chew Keng Yih, Ambalathingal George R, Rehan Sweera, Swaminathan Srividhya, Crooks Pauline, Le Texier Laetitia, Beagley Leone, Best Shannon, Solomon Matthew, Matthews Katherine K, Srihari Sriganesh, Neller Michelle A, Short Kirsty R, Khanna Rajiv, Smith Corey", "evidence": [ { "database": "IEDB", "id": "1312246", "url": "https://www.iedb.org/epitope/1312246" }, { "database": "IEDB", "id": "1313076", "url": "https://www.iedb.org/epitope/1313076" } ], "reference": [ { "type": "PubMed", "id": "35157735", "url": "https://glygen.org/publication/PubMed/35157735" } ] }, { "title": "SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells.", "journal": "Nature immunology", "date": "2022-05", "authors": "Minervina Anastasia A, Pogorelyy Mikhail V, Kirk Allison M, Crawford Jeremy Chase, Allen E Kaitlynn, Chou Ching-Heng, Mettelman Robert C, Allison Kim J, Lin Chun-Yang, Brice David C, Zhu Xun, Vegesana Kasi, Wu Gang, Trivedi Sanchit, Kottapalli Pratibha, Darnell Daniel, McNeely Suzanne, Olsen Scott R, Schultz-Cherry Stacey, Estepp Jeremie H, , McGargill Maureen A, Wolf Joshua, Thomas Paul G", "evidence": [ { "database": "IEDB", "id": "1324090", "url": "https://www.iedb.org/epitope/1324090" } ], "reference": [ { "type": "PubMed", "id": "35383307", "url": "https://glygen.org/publication/PubMed/35383307" } ] }, { "title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-05-09", "authors": "Titov Aleksei, Shaykhutdinova Regina, Shcherbakova Olga V, Serdyuk Yana V, Sheetikov Savely A, Zornikova Ksenia V, Maleeva Alexandra V, Khmelevskaya Alexandra, Dianov Dmitry V, Shakirova Naina T, Malko Dmitry B, Shkurnikov Maxim, Nersisyan Stepan, Tonevitsky Alexander, Khamaganova Ekaterina, Ershov Anton V, Osipova Elena Y, Nikolaev Ruslan V, Pershin Dmitry E, Vedmedskia Viktoria A, Maschan Michael, Ginanova Victoria R, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "5149", "url": "https://www.iedb.org/epitope/5149" }, { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" }, { "database": "IEDB", "id": "56634", "url": "https://www.iedb.org/epitope/56634" }, { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" }, { "database": "IEDB", "id": "1310684", "url": "https://www.iedb.org/epitope/1310684" }, { "database": "IEDB", "id": "1327887", "url": "https://www.iedb.org/epitope/1327887" }, { "database": "IEDB", "id": "1332258", "url": "https://www.iedb.org/epitope/1332258" } ], "reference": [ { "type": "PubMed", "id": "35389886", "url": "https://glygen.org/publication/PubMed/35389886" } ] }, { "title": "SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals.", "journal": "Nature microbiology", "date": "2022-05", "authors": "Lang-Meli Julia, Luxenburger Hendrik, Wild Katharina, Karl Vivien, Oberhardt Valerie, Salimi Alizei Elahe, Graeser Anne, Reinscheid Matthias, Roehlen Natascha, Reeg David B, Giese Sebastian, Ciminski Kevin, G\u00f6tz Veronika, August Dietrich, Rieg Siegbert, Waller Cornelius F, Wengenmayer Tobias, Staudacher Dawid, Huzly Daniela, Bengsch Bertram, Kochs Georg, Schwemmle Martin, Emmerich Florian, Boettler Tobias, Thimme Robert, Hofmann Maike, Neumann-Haefelin Christoph", "evidence": [ { "database": "IEDB", "id": "1075044", "url": "https://www.iedb.org/epitope/1075044" } ], "reference": [ { "type": "PubMed", "id": "35484232", "url": "https://glygen.org/publication/PubMed/35484232" } ] }, { "title": "High-resolution profiling of MHC II peptide presentation capacity reveals SARS-CoV-2 CD4 T cell targets and mechanisms of immune escape.", "journal": "Science advances", "date": "2022-04-29", "authors": "Obermair Franz-Josef, Renoux Florian, Heer Sebastian, Lee Chloe H, Cereghetti Nastassja, Loi Marisa, Maestri Giulia, Haldner Yannick, Wuigk Robin, Iosefson Ohad, Patel Pooja, Triebel Katherine, Kopf Manfred, Swain Joanna, Kisielow Jan", "evidence": [ { "database": "IEDB", "id": "1075030", "url": "https://www.iedb.org/epitope/1075030" }, { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" } ], "reference": [ { "type": "PubMed", "id": "35486722", "url": "https://glygen.org/publication/PubMed/35486722" } ] }, { "title": "Longitudinal Assessment of SARS-CoV-2-Specific T Cell Cytokine-Producing Responses for 1 Year Reveals Persistence of Multicytokine Proliferative Responses, with Greater Immunity Associated with Disease Severity.", "journal": "Journal of virology", "date": "2022-07-13", "authors": "Lin Jonah, Law Ryan, Korosec Chapin S, Zhou Christine, Koh Wan Hon, Ghaemi Mohammad Sajjad, Samaan Philip, Ooi Hsu Kiang, Matveev Vitaliy, Yue FengYun, Gingras Anne-Claude, Estacio Antonio, Buchholz Megan, Cheatley Patti Lou, Mohammadi Avid, Kaul Rupert, Pavinski Katerina, Mubareka Samira, McGeer Allison J, Leis Jerome A, Heffernan Jane M, Ostrowski Mario", "evidence": [ { "database": "IEDB", "id": "48051", "url": "https://www.iedb.org/epitope/48051" }, { "database": "IEDB", "id": "532894", "url": "https://www.iedb.org/epitope/532894" }, { "database": "IEDB", "id": "1310685", "url": "https://www.iedb.org/epitope/1310685" }, { "database": "IEDB", "id": "1312367", "url": "https://www.iedb.org/epitope/1312367" }, { "database": "IEDB", "id": "1312469", "url": "https://www.iedb.org/epitope/1312469" }, { "database": "IEDB", "id": "1312509", "url": "https://www.iedb.org/epitope/1312509" }, { "database": "IEDB", "id": "1312531", "url": "https://www.iedb.org/epitope/1312531" }, { "database": "IEDB", "id": 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Ekimoto Toru, Uemura Tomoko, Liu Kehong, Yui Moeko, Kono Nozomu, Aoki Junken, Ikeguchi Mitsunori, Noda Takeshi, Iwata So, Ohto Umeharu, Shimizu Toshiyuki", "evidence": [ { "database": "UniProtKB", "id": "P0DTC5", "url": "https://www.uniprot.org/uniprotkb/P0DTC5#ptm_processing" }, { "database": "UniProtKB", "id": "P0DTC5", "url": "https://www.uniprot.org/uniprotkb/P0DTC5" } ], "reference": [ { "type": "PubMed", "id": "35931673", "url": "https://glygen.org/publication/PubMed/35931673" } ] }, { "title": "Exosomal Vaccine Loading T Cell Epitope Peptides of SARS-CoV-2 Induces Robust CD8+ T Cell Response in HLA-A Transgenic Mice.", "journal": "International journal of nanomedicine", "date": "2022", "authors": "Shen An-Ran, Jin Xiao-Xiao, Tang Tao-Tao, Ding Yan, Liu Xiao-Tao, Zhong Xin, Wu Yan-Dan, Han Xue-Lian, Zhao Guang-Yu, Shen Chuan-Lai, Lv Lin-Li, Liu Bi-Cheng", "evidence": [ { "database": "IEDB", "id": "18219", "url": "https://www.iedb.org/epitope/18219" }, { "database": "IEDB", "id": 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"IEDB", "id": "5149", "url": "https://www.iedb.org/epitope/5149" }, { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" }, { "database": "IEDB", "id": "1330469", "url": "https://www.iedb.org/epitope/1330469" } ], "reference": [ { "type": "PubMed", "id": "36254196", "url": "https://glygen.org/publication/PubMed/36254196" } ] }, { "title": "Structure of SARS-CoV-2 M protein in lipid nanodiscs.", "journal": "eLife", "date": "2022-10-20", "authors": "Dolan Kimberly A, Dutta Mandira, Kern David M, Kotecha Abhay, Voth Gregory A, Brohawn Stephen G", "evidence": [ { "database": "UniProtKB", "id": "P0DTC5", "url": "https://www.uniprot.org/uniprotkb/P0DTC5#ptm_processing" }, { "database": "UniProtKB", "id": "P0DTC5", "url": "https://www.uniprot.org/uniprotkb/P0DTC5" } ], "reference": [ { "type": "PubMed", "id": "36264056", "url": "https://glygen.org/publication/PubMed/36264056" } ] }, { "title": "Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response.", "journal": "Communications biology", "date": "2022-12-09", "authors": "Zornikova Ksenia V, Khmelevskaya Alexandra, Sheetikov Savely A, Kiryukhin Dmitry O, Shcherbakova Olga V, Titov Aleksei, Zvyagin Ivan V, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "1075044", "url": "https://www.iedb.org/epitope/1075044" } ], "reference": [ { "type": "PubMed", "id": "36494499", "url": "https://glygen.org/publication/PubMed/36494499" } ] }, { "title": "Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19.", "journal": "Nature communications", "date": "2022-12-16", "authors": "Ogura Hideki, Gohda Jin, Lu Xiuyuan, Yamamoto Mizuki, Takesue Yoshio, Son Aoi, Doi Sadayuki, Matsushita Kazuyuki, Isobe Fumitaka, Fukuda Yoshihiro, Huang Tai-Ping, Ueno Takamasa, Mambo Naomi, Murakami Hiromoto, Kawaguchi Yasushi, Inoue Jun-Ichiro, Shirai Kunihiro, Yamasaki Sho, Hirata Jun-Ichi, Ishido Satoshi", "evidence": [ { "database": "IEDB", "id": "40677", "url": "https://www.iedb.org/epitope/40677" }, { "database": "IEDB", "id": "56634", "url": "https://www.iedb.org/epitope/56634" }, { "database": "IEDB", "id": "1313718", "url": "https://www.iedb.org/epitope/1313718" }, { "database": "IEDB", "id": "1313989", "url": "https://www.iedb.org/epitope/1313989" }, { "database": "IEDB", "id": "2154383", "url": "https://www.iedb.org/epitope/2154383" } ], "reference": [ { "type": "PubMed", "id": "36526616", "url": "https://glygen.org/publication/PubMed/36526616" } ] }, { "title": "Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes.", "journal": "Cell systems", "date": "2023-01-18", "authors": "Gfeller David, Schmidt Julien, Croce Giancarlo, Guillaume Philippe, Bobisse Sara, Genolet Raphael, Queiroz Lise, Cesbron Julien, Racle Julien, Harari Alexandre", "evidence": [ { "database": "IEDB", "id": "5150", "url": 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Rila, Randremanana Rindra Vatosoa, Sall Amadou Alpha, Seydi Moussa, Noirel Josselin, Moreau Gabriel, Simon Arnaud, Holenya Pavlo, Meyniel Jean-Philippe, Zagury Jean-Fran\u00e7ois, Schoenhals Matthieu", "evidence": [ { "database": "IEDB", "id": "1313207", "url": "https://www.iedb.org/epitope/1313207" }, { "database": "IEDB", "id": "1313811", "url": "https://www.iedb.org/epitope/1313811" } ], "reference": [ { "type": "PubMed", "id": "36646780", "url": "https://glygen.org/publication/PubMed/36646780" } ] }, { "title": "A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection.", "journal": "Nature", "date": "2023-08", "authors": "Augusto Danillo G, Murdolo Lawton D, Chatzileontiadou Demetra S M, Sabatino Joseph J, Yusufali Tasneem, Peyser Noah D, Butcher Xochitl, Kizer Kerry, Guthrie Karoline, Murray Victoria W, Pae Vivian, Sarvadhavabhatla Sannidhi, Beltran Fiona, Gill Gurjot S, Lynch Kara L, Yun Cassandra, Maguire Colin T, Peluso Michael J, Hoh Rebecca, Henrich Timothy J, Deeks Steven G, Davidson Michelle, Lu Scott, Goldberg Sarah A, Kelly J Daniel, Martin Jeffrey N, Vierra-Green Cynthia A, Spellman Stephen R, Langton David J, Dewar-Oldis Michael J, Smith Corey, Barnard Peter J, Lee Sulggi, Marcus Gregory M, Olgin Jeffrey E, Pletcher Mark J, Maiers Martin, Gras Stephanie, Hollenbach Jill A", "evidence": [ { "database": "IEDB", "id": "1324090", "url": "https://www.iedb.org/epitope/1324090" } ], "reference": [ { "type": "PubMed", "id": "37468623", "url": "https://glygen.org/publication/PubMed/37468623" } ] }, { "title": "Phase I/II trial of a peptide-based COVID-19 T-cell activator in patients with B-cell deficiency.", "journal": "Nature communications", "date": "2023-08-18", "authors": "Heitmann Jonas S, Tandler Claudia, Marconato Maddalena, Nelde Annika, Habibzada Timorshah, Rittig Susanne M, Tegeler Christian M, Maringer Yacine, Jaeger Simon U, Denk Monika, Richter Marion, Oezbek Melek T, Wiesm\u00fcller Karl-Heinz, Bauer Jens, Rieth Jonas, Wacker Marcel, Schroeder Sarah M, Hoenisch Gravel Naomi, Scheid Jonas, M\u00e4rklin Melanie, Henrich Annika, Klimovich Boris, Clar Kim L, Lutz Martina, Holzmayer Samuel, H\u00f6rber Sebastian, Peter Andreas, Meisner Christoph, Fischer Imma, L\u00f6ffler Markus W, Peuker Caroline Anna, Habringer Stefan, Goetze Thorsten O, J\u00e4ger Elke, Rammensee Hans-Georg, Salih Helmut R, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" } ], "reference": [ { "type": "PubMed", "id": "37596280", "url": "https://glygen.org/publication/PubMed/37596280" } ] }, { "title": "Detection of Antibodies against Endemic and SARS-CoV-2 Coronaviruses with Short Peptide Epitopes.", "journal": "Vaccines", "date": "2023-08-23", "authors": "Szardenings Michael, Delaroque Nicolas, Kern Karolin, Ramirez-Caballero Lisbeth, Puder Marcus, Ehrentreich-F\u00f6rster Eva, Beige Joachim, Z\u00fcrner Sebastian, Popp Georg, Wolf Johannes, Borte Stephan", "evidence": [ { 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SARS-CoV-2-Specific T Cells.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2024-03-01", "authors": "Maino Anthony, Amen Axelle, Plumas Jo\u00ebl, Bouquet Lucie, Deschamps Marina, Saas Philippe, Chaperot Laurence, Manches Olivier", "evidence": [ { "database": "IEDB", "id": "59778", "url": "https://www.iedb.org/epitope/59778" } ], "reference": [ { "type": "PubMed", "id": "38214610", "url": "https://glygen.org/publication/PubMed/38214610" } ] }, { "title": "mRNA-1273 vaccinated inflammatory bowel disease patients receiving TNF inhibitors develop broad and robust SARS-CoV-2-specific CD8+ T cell responses.", "journal": "Journal of autoimmunity", "date": "2024-04", "authors": "van den Dijssel Jet, Duurland Mari\u00ebl C, Konijn Veronique Al, Kummer Laura Yl, Hagen Ruth R, Kuijper Lisan H, Wieske Luuk, van Dam Koos Pj, Stalman Eileen W, Steenhuis Maurice, Geerdes Dionne M, Mok Juk Yee, Kragten Angela Hm, Menage Charlotte, Koets Lianne, Veldhuisen Barbera, Verstegen Niels Jm, van der Schoot C Ellen, van Esch Wim Je, D'Haens Geert Ram, L\u00f6wenberg Mark, Volkers Adriaan G, Rispens Theo, Kuijpers Taco W, Eftimov Filip, van Gisbergen Klaas Pjm, van Ham S Marieke, Ten Brinke Anja, van de Sandt Carolien E,", "evidence": [ { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" } ], "reference": [ { "type": "PubMed", "id": "38387105", "url": "https://glygen.org/publication/PubMed/38387105" } ] }, { "title": "High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4+ and CD8+ memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Coulon Pierre-Gregoire, Prakash Swayam, Dhanushkodi Nisha R, Srivastava Ruchi, Zayou Latifa, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Nesburn Anthony B, Kuppermann Baruch D, Bahraoui Elmostafa, Vahed Hawa, Gil Daniel, Jones Trevor M, Ulmer Jeffrey B, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "1310622", "url": "https://www.iedb.org/epitope/1310622" }, { "database": "IEDB", "id": "1330469", "url": "https://www.iedb.org/epitope/1330469" }, { "database": "IEDB", "id": "1332347", "url": "https://www.iedb.org/epitope/1332347" } ], "reference": [ { "type": "PubMed", "id": "38605956", "url": "https://glygen.org/publication/PubMed/38605956" } ] }, { "title": "Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set.", "journal": "Science advances", "date": "2024-04-12", "authors": "Kristensen Nikolaj Pagh, Dionisio Edoardo, Bentzen Amalie Kai, Tamhane Tripti, Kemming Janine Sophie, Nos Grigorii, Voss Lasse Frank, Hansen Ulla Kring, Lauer Georg Michael, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "64710", "url": "https://www.iedb.org/epitope/64710" }, { "database": "IEDB", 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Ting, Wang Xi, Jin Ronghua, Zhou Jikun, Gao George F, Liu Jun", "evidence": [ { "database": "IEDB", "id": "5149", "url": "https://www.iedb.org/epitope/5149" }, { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" } ], "reference": [ { "type": "PubMed", "id": "38866784", "url": "https://glygen.org/publication/PubMed/38866784" } ] }, { "title": "Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8+ T-Cell Response in Patients with Severe Symptoms.", "journal": "Vaccines", "date": "2024-06-18", "authors": "Mart\u00edn-Mart\u00edn Cristina, Del Riego Estefan\u00eda Salgado, Casti\u00f1eira Jose R Vidal, Zapico-Gonzalez Maria Soledad, Rodr\u00edguez-P\u00e9rez Mercedes, Corte-Iglesias Viviana, Saiz Maria Laura, Diaz-Bulnes Paula, Escudero Dolores, Su\u00e1rez-Alvarez Beatriz, L\u00f3pez-Larrea Carlos", "evidence": [ { "database": "IEDB", "id": "5150", "url": "https://www.iedb.org/epitope/5150" } ], "reference": [ { "type": "PubMed", "id": "38932408", 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"monoisotopic_mass": 7273.0 }, "refseq": { "ac": "YP_009724394", "name": "ORF6 protein", "summary": "", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724394" }, "gene_names": [ { "name": "6", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ] } ], "protein_names": [ { "name": "ORF6 protein", "type": "recommended", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] }, { "name": "Accessory protein 6", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 6", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] }, { "name": "ORF6 protein", "type": "synonym", "evidence": [ { "id": "YP_009724394", "database": "RefSeq", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724394" } ] }, { "name": "ORF6", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] }, { "name": "Protein X3", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] }, { "name": "ns6", "type": "synonym", "evidence": [ { "id": "P0DTC6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#names_and_taxonomy" } ] } ], "function": [ { "annotation": "Disrupts bidirectional nucleocytoplasmic transport by interacting with the host RAE1-NUP98 complex (PubMed:33360543, PubMed:33849972). Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane (PubMed:32979938). Retention of import factors at the ER/Golgi membrane leads to a loss of transport into the nucleus (By similarity). Prevents STAT1 nuclear translocation in response to interferon signaling, thus blocking the expression of interferon stimulated genes (ISGs) that display multiple antiviral activities (PubMed:33097660). Suppresses IFN-beta production possibly by blocking IRF3 nuclear translocation (PubMed:32979938). Might induce accumulation of host HNRNPA1 (PubMed:33360543).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6#function" }, { "database": "UniProtKB", "id": "P59634", "url": "https://www.uniprot.org/uniprotkb/P59634#function" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "33360543", "url": "https://glygen.org/publication/PubMed/33360543" }, { "database": "PubMed", "id": "33097660", "url": "https://glygen.org/publication/PubMed/33097660" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "annotation": "May play a role in viral double membrane vesicles networks to enhance viral replication.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6#function" }, { "database": "PubMed", "id": "35187564", "url": "https://glygen.org/publication/PubMed/35187564" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "COVID-19", "description": "A disease caused by infection with severe acute respiratory syndrome coronavirus 2." }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "coronavirus disease 2019", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2 infectious disease", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-CoV-2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "SARS-coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "beta-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "betacoronavirus", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoV", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-CoVs", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "-coronavirus", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "GLY_000490", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000490" } ] } ], "snv": [], "mutagenesis": [ { "start_pos": 18, "end_pos": 24, "sequence_org": "IMRTFKV", "sequence_mut": "AAAAAAA", "comment": "Complete loss of Golgi localization.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "35187564", "url": "https://glygen.org/publication/PubMed/35187564" } ] }, { "start_pos": 18, "end_pos": 24, "sequence_org": "IMRTFKV", "sequence_mut": "", "comment": "Complete loss of Golgi localization.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "35187564", "url": "https://glygen.org/publication/PubMed/35187564" } ] }, { "start_pos": 1, "end_pos": 16, "sequence_org": "MFHLVDFQVTIAEILL", "sequence_mut": "", "comment": "Retains interaction with human NUP98-RAE1 complex. Increases down-regulation of protein expression of newly transcribed genes in host cell.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "start_pos": 22, "end_pos": 30, "sequence_org": "FKVSIWNLD", "sequence_mut": "", "comment": "Retains interaction with human NUP98-RAE1 complex. Increases down-regulation of protein expression of newly transcribed genes in host cell.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "start_pos": 38, "end_pos": 61, "sequence_org": "KNLSKSLTENKYSQLDEEQPMEID", "sequence_mut": "", "comment": "Loss of interaction with human NUP98-RAE1 complex which suppresses the down-regulation of protein expression of newly transcribed genes in the host cell.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "start_pos": 50, "end_pos": 61, "sequence_org": "SQLDEEQPMEID", "sequence_mut": "", "comment": "Loss of interaction with human NUP98-RAE1 complex which suppresses the down-regulation of protein expression of newly transcribed genes in the host cell.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "start_pos": 58, "end_pos": 58, "sequence_org": "M", "sequence_mut": "A", "comment": "Loss of interaction with human NUP98-RAE1 complex which suppresses the mRNA accumulation in the nucleus, the down-regulation of protein expression of newly transcribed genes in the host cell and blockade on nuclear import on a broad range of host factors.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "35096974", "url": "https://glygen.org/publication/PubMed/35096974" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "start_pos": 58, "end_pos": 58, "sequence_org": "M", "sequence_mut": "R", "comment": "Complete loss of binding to the NUP98-RAE1 complex and IFN antagonistic function.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "35096974", "url": "https://glygen.org/publication/PubMed/35096974" }, { "database": "PubMed", "id": "33097660", "url": "https://glygen.org/publication/PubMed/33097660" } ] }, { "start_pos": 61, "end_pos": 61, "sequence_org": "D", "sequence_mut": "DYP", "comment": "Does not affect repression of reporter protein expression.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" }, { "database": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] } ], "expression_tissue": [], "expression_disease": [], "species": [ { "name": "Severe acute respiratory syndrome coronavirus 2", "taxid": 2697049, "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "common_name": "2019-nCoV", "glygen_name": "SARS-CoV-2", "reference_species": "Severe acute respiratory syndrome coronavirus 2 [2697049]" } ], "gene": [ { "name": "", "url": "https://www.uniprot.org/uniprotkb/P0DTC6", "locus": {} } ], "crossref": [ { "id": "43740572", "url": "https://www.ncbi.nlm.nih.gov/gene/43740572", "database": "GeneID", "categories": [ "Genome Annotation" ] }, { "id": "7F60", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=7F60&bu=0", "database": "iCn3D", "categories": [ "3D Structure" ] }, { "id": "7VPH", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=7VPH&bu=0", "database": "iCn3D", "categories": [ "3D Structure" ] }, { "id": "1310517", "url": "https://www.iedb.org/epitope/1310517", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1310558", "url": "https://www.iedb.org/epitope/1310558", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1310776", "url": "https://www.iedb.org/epitope/1310776", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1310804", "url": "https://www.iedb.org/epitope/1310804", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1330789", "url": "https://www.iedb.org/epitope/1330789", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1332260", "url": "https://www.iedb.org/epitope/1332260", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1332625", "url": "https://www.iedb.org/epitope/1332625", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1333954", "url": "https://www.iedb.org/epitope/1333954", "database": "IEDB", "categories": [ "Other" ] }, { "id": "1597178", "url": "https://www.iedb.org/epitope/1597178", "database": "IEDB", "categories": [ "Other" ] }, { "id": "2134209", "url": "https://www.iedb.org/epitope/2134209", "database": "IEDB", "categories": [ "Other" ] }, { "id": "2134271", "url": "https://www.iedb.org/epitope/2134271", "database": "IEDB", "categories": [ "Other" ] }, { "id": "2252835", "url": "https://www.iedb.org/epitope/2252835", "database": "IEDB", "categories": [ "Other" ] }, { "id": "24313", "url": "https://www.iedb.org/epitope/24313", "database": "IEDB", "categories": [ "Other" ] }, { "id": "IPR022736", "url": "https://www.ebi.ac.uk/interpro/entry/IPR022736", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "pdb_00007f60", "url": "https://www.rcsb.org/structure/pdb_00007f60", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "pdb_00007vph", "url": "https://www.rcsb.org/structure/pdb_00007vph", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7F60", "url": "https://www.rcsb.org/structure/7F60", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7VPH", "url": "https://www.rcsb.org/structure/7VPH", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "PF12133", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF12133", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "YP_009724394", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724394", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC6-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC6-1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC6", "url": "https://viral.glycomics.ku.dk/viewer/?uniprot=P0DTC6", "database": "Viral Glycome", "categories": [ "Organism-specific" ] } ], "sequence": { "sequence": "MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID", "length": 61, "header": "sp|P0DTC6-1|NS6_SARS2 Isoform 1 of ORF6 protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC6-1" }, "isoforms": [ { "isoform_ac": "P0DTC6-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC6/entry#P0DTC6-1", "sequence": { "sequence": "MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID", "length": 61, "header": "sp|P0DTC6-1|NS6_SARS2 Isoform 1 of ORF6 protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC6-1" }, "locus": {} } ], "glycosylation": [], "phosphorylation": [], "glycation": [], "keywords": [], "publication": [ { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "Evasion of Type I Interferon by SARS-CoV-2.", "journal": "Cell reports", "date": "2020", "authors": "Xia H, Cao Z, Xie X, Zhang X, Chen JY, Wang H, Menachery VD, Rajsbaum R, Shi PY", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310517", "url": "https://www.iedb.org/epitope/1310517" }, { "database": "IEDB", "id": "1310776", "url": "https://www.iedb.org/epitope/1310776" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2020", "authors": "Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, Garcia-Sastre A", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "33097660", "url": "https://glygen.org/publication/PubMed/33097660" } ] }, { "title": "Overexpression of SARS-CoV-2 protein ORF6 dislocates RAE1 and NUP98 from the nuclear pore complex.", "journal": "Biochemical and biophysical research communications", "date": "2021", "authors": "Kato K, Ikliptikawati DK, Kobayashi A, Kondo H, Lim K, Hazawa M, Wong RW", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "33360543", "url": "https://glygen.org/publication/PubMed/33360543" } ] }, { "title": "SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98.", "journal": "mBio", "date": "2021", "authors": "Addetia A, Lieberman NAP, Phung Q, Hsiang TY, Xie H, Roychoudhury P, Shrestha L, Loprieno MA, Huang ML, Gale M Jr, Jerome KR, Greninger AL", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "33849972", "url": "https://glygen.org/publication/PubMed/33849972" } ] }, { "title": "SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.", "journal": "Science immunology", "date": "2021-04-14", "authors": "Saini Sunil Kumar, Hersby Ditte Stampe, Tamhane Tripti, Povlsen Helle Rus, Amaya Hernandez Susana Patricia, Nielsen Morten, Gang Anne Ortved, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" }, { "database": "IEDB", "id": "1310804", "url": "https://www.iedb.org/epitope/1310804" }, { "database": "IEDB", "id": "1332260", "url": "https://www.iedb.org/epitope/1332260" }, { "database": "IEDB", "id": "1332625", "url": "https://www.iedb.org/epitope/1332625" }, { "database": "IEDB", "id": "1333954", "url": "https://www.iedb.org/epitope/1333954" } ], "reference": [ { "type": "PubMed", "id": "33853928", "url": "https://glygen.org/publication/PubMed/33853928" } ] }, { "title": "Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2021-06-01", "authors": "Prakash Swayam, Srivastava Ruchi, Coulon Pierre-Gregoire, Dhanushkodi Nisha R, Chentoufi Aziz A, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Buchmeier Michael J, Bouziane Mohammed, Nesburn Anthony B, Kuppermann Baruch D, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" }, { "database": "IEDB", "id": "1330789", "url": "https://www.iedb.org/epitope/1330789" } ], "reference": [ { "type": "PubMed", "id": "33911008", "url": "https://glygen.org/publication/PubMed/33911008" } ] }, { "title": "Large-Scale Identification of T-Cell Epitopes Derived From Severe Acute Respiratory Syndrome Coronavirus 2 for the Development of Peptide Vaccines Against Coronavirus Disease 2019.", "journal": "The Journal of infectious diseases", "date": "2021-09-17", "authors": "Ma Yipeng, Liu Fenglan, Lin Tong, Chen Lei, Jiang Aixin, Tian Geng, Nielsen Morten, Wang Mingjun", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" }, { "database": "IEDB", "id": "1333954", "url": "https://www.iedb.org/epitope/1333954" } ], "reference": [ { "type": "PubMed", "id": "34145459", "url": "https://glygen.org/publication/PubMed/34145459" } ] }, { "title": "Profiling CD8+ T\u00a0cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.", "journal": "Cell reports", "date": "2021-09-14", "authors": "Zhang Hang, Deng Shasha, Ren Liting, Zheng Peiyi, Hu Xiaowen, Jin Tengchuan, Tan Xu", "evidence": [ { "database": "IEDB", "id": "1597178", "url": "https://www.iedb.org/epitope/1597178" } ], "reference": [ { "type": "PubMed", "id": "34506741", "url": "https://glygen.org/publication/PubMed/34506741" } ] }, { "title": "Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2.", "journal": "Science immunology", "date": "2022-01-21", "authors": "Francis Joshua M, Leistritz-Edwards Del, Dunn Augustine, Tarr Christina, Lehman Jesse, Dempsey Conor, Hamel Andrew, Rayon Violeta, Liu Gang, Wang Yuntong, Wille Marcos, Durkin Melissa, Hadley Kane, Sheena Aswathy, Roscoe Benjamin, Ng Mark, Rockwell Graham, Manto Margaret, Gienger Elizabeth, Nickerson Joshua, , Moarefi Amir, Noble Michael, Malia Thomas, Bardwell Philip D, Gordon William, Swain Joanna, Skoberne Mojca, Sauer Karsten, Harris Tim, Goldrath Ananda W, Shalek Alex K, Coyle Anthony J, Benoist Christophe, Pregibon Daniel C", "evidence": [ { "database": "IEDB", "id": "1310558", "url": "https://www.iedb.org/epitope/1310558" }, { "database": "IEDB", "id": "1332625", "url": "https://www.iedb.org/epitope/1332625" }, { "database": "IEDB", "id": "2134209", "url": "https://www.iedb.org/epitope/2134209" }, { "database": "IEDB", "id": "2134271", "url": "https://www.iedb.org/epitope/2134271" } ], "reference": [ { "type": "PubMed", "id": "34793243", "url": "https://glygen.org/publication/PubMed/34793243" } ] }, { "title": "Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.", "journal": "Frontiers in molecular biosciences", "date": "2021", "authors": "Li T, Wen Y, Guo H, Yang T, Yang H, Ji X", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "35096974", "url": "https://glygen.org/publication/PubMed/35096974" } ] }, { "title": "Decoupling SARS-CoV-2 ORF6 localization and interferon antagonism.", "journal": "Journal of cell science", "date": "2022", "authors": "Wong HT, Cheung V, Salamango DJ", "evidence": [ { "database": "UniProtKB", "id": "P0DTC6", "url": "https://www.uniprot.org/uniprotkb/P0DTC6" } ], "reference": [ { "type": "PubMed", "id": "35187564", "url": "https://glygen.org/publication/PubMed/35187564" } ] }, { "title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-05-09", "authors": "Titov Aleksei, Shaykhutdinova Regina, Shcherbakova Olga V, Serdyuk Yana V, Sheetikov Savely A, Zornikova Ksenia V, Maleeva Alexandra V, Khmelevskaya Alexandra, Dianov Dmitry V, Shakirova Naina T, Malko Dmitry B, Shkurnikov Maxim, Nersisyan Stepan, Tonevitsky Alexander, Khamaganova Ekaterina, Ershov Anton V, Osipova Elena Y, Nikolaev Ruslan V, Pershin Dmitry E, Vedmedskia Viktoria A, Maschan Michael, Ginanova Victoria R, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" } ], "reference": [ { "type": "PubMed", "id": "35389886", "url": "https://glygen.org/publication/PubMed/35389886" } ] }, { "title": "Parallel detection of SARS-CoV-2 epitopes reveals dynamic immunodominance profiles of CD8+ T memory cells in convalescent COVID-19 donors.", "journal": "Clinical & translational immunology", "date": "2022", "authors": "van den Dijssel Jet, Hagen Ruth R, de Jongh Rivka, Steenhuis Maurice, Rispens Theo, Geerdes Dionne M, Mok Juk Yee, Kragten Angela Hm, Duurland Mari\u00ebl C, Verstegen Niels Jm, van Ham S Marieke, van Esch Wim Je, van Gisbergen Klaas Pjm, Hombrink Pleun, Ten Brinke Anja, van de Sandt Carolien E", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" } ], "reference": [ { "type": "PubMed", "id": "36254196", "url": "https://glygen.org/publication/PubMed/36254196" } ] }, { "title": "The HLA-II immunopeptidome of SARS-CoV-2.", "journal": "Cell reports", "date": "2024-01-23", "authors": "Weingarten-Gabbay Shira, Chen Da-Yuan, Sarkizova Siranush, Taylor Hannah B, Gentili Matteo, Hernandez Gabrielle M, Pearlman Leah R, Bauer Matthew R, Rice Charles M, Clauser Karl R, Hacohen Nir, Carr Steven A, Abelin Jennifer G, Saeed Mohsan, Sabeti Pardis C", "evidence": [ { "database": "IEDB", "id": "2252835", "url": "https://www.iedb.org/epitope/2252835" } ], "reference": [ { "type": "PubMed", "id": "38117652", "url": "https://glygen.org/publication/PubMed/38117652" } ] }, { "title": "High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4+ and CD8+ memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Coulon Pierre-Gregoire, Prakash Swayam, Dhanushkodi Nisha R, Srivastava Ruchi, Zayou Latifa, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Nesburn Anthony B, Kuppermann Baruch D, Bahraoui Elmostafa, Vahed Hawa, Gil Daniel, Jones Trevor M, Ulmer Jeffrey B, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "24313", "url": "https://www.iedb.org/epitope/24313" }, { "database": "IEDB", "id": "1330789", "url": "https://www.iedb.org/epitope/1330789" } ], "reference": [ { "type": "PubMed", "id": "38605956", "url": "https://glygen.org/publication/PubMed/38605956" } ] } ], "pathway": [], "orthologs": [ { "uniprot_canonical_ac": "P59634-1", "protein_name": "ORF6 protein", "gene_name": "", "tax_id": 694009, "organism": "Severe acute respiratory syndrome-related coronavirus", "sequence": { "sequence": "MFHLVDFQVTIAEILIIIMRTFRIAIWNLDVIISSIVRQLFKPLTKKNYSELDDEEPMELDYP", "length": 63 }, 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"https://www.ebi.ac.uk/interpro/entry/IPR044871", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "pdb_00006w37", "url": "https://www.rcsb.org/structure/pdb_00006w37", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "pdb_00007ci3", "url": "https://www.rcsb.org/structure/pdb_00007ci3", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "6W37", "url": "https://www.rcsb.org/structure/6W37", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7CI3", "url": "https://www.rcsb.org/structure/7CI3", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "PF08779", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08779", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "YP_009724395", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724395", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC7-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC7-1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTC7", "url": "https://viral.glycomics.ku.dk/viewer/?uniprot=P0DTC7", "database": "Viral Glycome", "categories": [ "Organism-specific" ] } ], "sequence": { "sequence": "MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE", "length": 121, "header": "sp|P0DTC7-1|NS7A_SARS2 Isoform 1 of ORF7a protein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN= PE=1 SV=1 CANONICAL=P0DTC7-1" }, "isoforms": [ { "isoform_ac": "P0DTC7-1", "url": "https://www.uniprot.org/uniprotkb/P0DTC7/entry#P0DTC7-1", "sequence": { "sequence": "MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE", "length": 121, "header": "sp|P0DTC7-1|NS7A_SARS2 Isoform 1 of ORF7a protein OS=Severe 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Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "73668", "url": "https://www.iedb.org/epitope/73668" }, { "database": "IEDB", "id": "1310732", "url": "https://www.iedb.org/epitope/1310732" }, { "database": "IEDB", "id": "1310741", "url": "https://www.iedb.org/epitope/1310741" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020.", "journal": "Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin", "date": "2021", "authors": "Leung K, Shum MH, Leung GM, Lam TT, Wu JT", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "33413740", "url": "https://glygen.org/publication/PubMed/33413740" } ] }, { "title": "SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals.", "journal": "The Journal of clinical investigation", "date": "2021-03-01", "authors": "Kared Hassen, Redd Andrew D, Bloch Evan M, Bonny Tania S, Sumatoh Hermi, Kairi Faris, Carbajo Daniel, Abel Brian, Newell Evan W, Bettinotti Maria P, Benner Sarah E, Patel Eshan U, Littlefield Kirsten, Laeyendecker Oliver, Shoham Shmuel, Sullivan David, Casadevall Arturo, Pekosz Andrew, Nardin Alessandra, Fehlings Michael, Tobian Aaron Ar, Quinn Thomas C", "evidence": [ { "database": "IEDB", "id": "1330565", "url": "https://www.iedb.org/epitope/1330565" } ], "reference": [ { "type": "PubMed", "id": "33427749", "url": "https://glygen.org/publication/PubMed/33427749" } ] }, { "title": "Ubiquitination of SARS-CoV-2 ORF7a promotes antagonism of interferon response.", "journal": "Cellular & molecular immunology", "date": "2021", "authors": "Cao Z, Xia H, Rajsbaum R, Xia X, Wang H, Shi PY", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "33473190", "url": "https://glygen.org/publication/PubMed/33473190" } ] }, { "title": "Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes.", "journal": "IScience", "date": "2021", "authors": "Zhou Ziliang, Huang Chunliu, Zhou Zhechong, Huang Zhaoxia, Su Lili, Kang Sisi, Chen Xiaoxue, Chen Qiuyue, He Suhua, Rong Xia, Xiao Fei, Chen Jun, Chen Shoudeng", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "33615195", "url": "https://glygen.org/publication/PubMed/33615195" } ] }, { "title": "SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.", "journal": "Science immunology", "date": "2021-04-14", "authors": "Saini Sunil Kumar, Hersby Ditte Stampe, Tamhane Tripti, Povlsen Helle Rus, Amaya Hernandez Susana Patricia, Nielsen Morten, Gang Anne Ortved, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "24466", "url": "https://www.iedb.org/epitope/24466" }, { "database": "IEDB", "id": "1331581", "url": "https://www.iedb.org/epitope/1331581" }, { "database": "IEDB", "id": "1331926", "url": "https://www.iedb.org/epitope/1331926" }, { "database": "IEDB", "id": "1331954", "url": "https://www.iedb.org/epitope/1331954" }, { "database": "IEDB", "id": "1332462", "url": "https://www.iedb.org/epitope/1332462" }, { "database": "IEDB", "id": "1332642", "url": "https://www.iedb.org/epitope/1332642" }, { "database": "IEDB", "id": "1333721", "url": "https://www.iedb.org/epitope/1333721" } ], "reference": [ { "type": "PubMed", "id": "33853928", "url": "https://glygen.org/publication/PubMed/33853928" } ] }, { "title": "Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2021-06-01", "authors": "Prakash Swayam, Srivastava Ruchi, Coulon Pierre-Gregoire, Dhanushkodi Nisha R, Chentoufi Aziz A, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Buchmeier Michael J, Bouziane Mohammed, Nesburn Anthony B, Kuppermann Baruch D, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "1310643", "url": "https://www.iedb.org/epitope/1310643" }, { "database": "IEDB", "id": "1332359", "url": "https://www.iedb.org/epitope/1332359" }, { "database": "IEDB", "id": "1333722", "url": "https://www.iedb.org/epitope/1333722" } ], "reference": [ { "type": "PubMed", "id": "33911008", "url": "https://glygen.org/publication/PubMed/33911008" } ] }, { "title": "Functional landscape of SARS-CoV-2 cellular restriction.", "journal": "Molecular cell", "date": "2021", "authors": "Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, Garcia-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "33930332", "url": "https://glygen.org/publication/PubMed/33930332" } ] }, { "title": "Profiling SARS-CoV-2 HLA-I peptidome reveals T\u00a0cell epitopes from out-of-frame ORFs.", "journal": "Cell", "date": "2021-07-22", "authors": "Weingarten-Gabbay Shira, Klaeger Susan, Sarkizova Siranush, Pearlman Leah R, Chen Da-Yuan, Gallagher Kathleen M E, Bauer Matthew R, Taylor Hannah B, Dunn W Augustine, Tarr Christina, Sidney John, Rachimi Suzanna, Conway Hasahn L, Katsis Katelin, Wang Yuntong, Leistritz-Edwards Del, Durkin Melissa R, Tomkins-Tinch Christopher H, Finkel Yaara, Nachshon Aharon, Gentili Matteo, Rivera Keith D, Carulli Isabel P, Chea Vipheaviny A, Chandrashekar Abishek, Bozkus Cansu Cimen, Carrington Mary, , Bhardwaj Nina, Barouch Dan H, Sette Alessandro, Maus Marcela V, Rice Charles M, Clauser Karl R, Keskin Derin B, Pregibon Daniel C, Hacohen Nir, Carr Steven A, Abelin Jennifer G, Saeed Mohsan, Sabeti Pardis C", "evidence": [ { "database": "IEDB", "id": "1310507", "url": "https://www.iedb.org/epitope/1310507" } ], "reference": [ { "type": "PubMed", "id": "34171305", "url": "https://glygen.org/publication/PubMed/34171305" } ] }, { "title": "Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2.", "journal": "Science immunology", "date": "2022-01-21", "authors": "Francis Joshua M, Leistritz-Edwards Del, Dunn Augustine, Tarr Christina, Lehman Jesse, Dempsey Conor, Hamel Andrew, Rayon Violeta, Liu Gang, Wang Yuntong, Wille Marcos, Durkin Melissa, Hadley Kane, Sheena Aswathy, Roscoe Benjamin, Ng Mark, Rockwell Graham, Manto Margaret, Gienger Elizabeth, Nickerson Joshua, , Moarefi Amir, Noble Michael, Malia Thomas, Bardwell Philip D, Gordon William, Swain Joanna, Skoberne Mojca, Sauer Karsten, Harris Tim, Goldrath Ananda W, Shalek Alex K, Coyle Anthony J, Benoist Christophe, Pregibon Daniel C", "evidence": [ { "database": "IEDB", "id": "31846", "url": "https://www.iedb.org/epitope/31846" }, { "database": "IEDB", "id": "2134041", "url": "https://www.iedb.org/epitope/2134041" }, { "database": "IEDB", "id": "2134042", "url": "https://www.iedb.org/epitope/2134042" }, { "database": "IEDB", "id": "2134047", "url": "https://www.iedb.org/epitope/2134047" }, { "database": "IEDB", "id": "2134125", "url": "https://www.iedb.org/epitope/2134125" }, { "database": "IEDB", "id": "2134135", "url": "https://www.iedb.org/epitope/2134135" } ], "reference": [ { "type": "PubMed", "id": "34793243", "url": "https://glygen.org/publication/PubMed/34793243" } ] }, { "title": "SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion.", "journal": "FEBS J.", "date": "2022", "authors": "Quaglia Federica, Salladini Edoardo, Carraro Marco, Minervini Giovanni, Tosatto Silvio C E, Le Mercier Philippe", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "35108439", "url": "https://glygen.org/publication/PubMed/35108439" } ] }, { "title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-05-09", "authors": "Titov Aleksei, Shaykhutdinova Regina, Shcherbakova Olga V, Serdyuk Yana V, Sheetikov Savely A, Zornikova Ksenia V, Maleeva Alexandra V, Khmelevskaya Alexandra, Dianov Dmitry V, Shakirova Naina T, Malko Dmitry B, Shkurnikov Maxim, Nersisyan Stepan, Tonevitsky Alexander, Khamaganova Ekaterina, Ershov Anton V, Osipova Elena Y, Nikolaev Ruslan V, Pershin Dmitry E, Vedmedskia Viktoria A, Maschan Michael, Ginanova Victoria R, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "1310741", "url": "https://www.iedb.org/epitope/1310741" } ], "reference": [ { "type": "PubMed", "id": "35389886", "url": "https://glygen.org/publication/PubMed/35389886" } ] }, { "title": "SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals.", "journal": "Nature microbiology", "date": "2022-05", "authors": "Lang-Meli Julia, Luxenburger Hendrik, Wild Katharina, Karl Vivien, Oberhardt Valerie, Salimi Alizei Elahe, Graeser Anne, Reinscheid Matthias, Roehlen Natascha, Reeg David B, Giese Sebastian, Ciminski Kevin, G\u00f6tz Veronika, August Dietrich, Rieg Siegbert, Waller Cornelius F, Wengenmayer Tobias, Staudacher Dawid, Huzly Daniela, Bengsch Bertram, Kochs Georg, Schwemmle Martin, Emmerich Florian, Boettler Tobias, Thimme Robert, Hofmann Maike, Neumann-Haefelin Christoph", "evidence": [ { "database": "IEDB", "id": "1330565", "url": "https://www.iedb.org/epitope/1330565" } ], "reference": [ { "type": "PubMed", "id": "35484232", "url": "https://glygen.org/publication/PubMed/35484232" } ] }, { "title": "Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response.", "journal": "Communications biology", "date": "2022-12-09", "authors": "Zornikova Ksenia V, Khmelevskaya Alexandra, Sheetikov Savely A, Kiryukhin Dmitry O, Shcherbakova Olga V, Titov Aleksei, Zvyagin Ivan V, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "1310741", "url": "https://www.iedb.org/epitope/1310741" } ], "reference": [ { "type": "PubMed", "id": "36494499", "url": "https://glygen.org/publication/PubMed/36494499" } ] }, { "title": "SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2023-01-03", "authors": "Arshad Najla, Laurent-Rolle Maudry, Ahmed Wesam S, Hsu Jack Chun-Chieh, Mitchell Susan M, Pawlak Joanna, Sengupta Debrup, Biswas Kabir H, Cresswell Peter", "evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" } ], "reference": [ { "type": "PubMed", "id": "36574644", "url": "https://glygen.org/publication/PubMed/36574644" } ] }, { "title": "Novel neutralizing chicken IgY antibodies targeting 17 potent conserved peptides identified by SARS-CoV-2 proteome microarray, and future prospects.", "journal": "Frontiers in immunology", "date": "2022", "authors": "Li Jin, Liang Te, Hei Ailian, Wang Xiangbin, Li Huijun, Yu Xiaobo, Zhao Rui, Gao Peng, Fang Cong, Zhou Ji, Li Maogang, He Ellen, Skog Sven", "evidence": [ { "database": "IEDB", "id": "2150872", "url": "https://www.iedb.org/epitope/2150872" } ], "reference": [ { "type": "PubMed", "id": "36618358", "url": "https://glygen.org/publication/PubMed/36618358" } ] }, { "title": "A multifaceted approach for identification, validation, and immunogenicity of naturally processed and in silico-predicted highly conserved SARS-CoV-2 peptides.", "journal": "Vaccine", "date": "2024-01-12", "authors": "Ratishvili Tamar, Quach Huy Quang, Haralambieva Iana H, Suryawanshi Yogesh R, Ovsyannikova Inna G, Kennedy Richard B, Poland Gregory A", "evidence": [ { "database": "IEDB", "id": "1310893", "url": "https://www.iedb.org/epitope/1310893" } ], "reference": [ { "type": "PubMed", "id": "38105139", "url": "https://glygen.org/publication/PubMed/38105139" } ] }, { "title": "High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4+ and CD8+ memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Coulon Pierre-Gregoire, Prakash Swayam, Dhanushkodi Nisha R, Srivastava Ruchi, Zayou Latifa, Tifrea Delia F, Edwards Robert A, Figueroa Cesar J, Schubl Sebastian D, Hsieh Lanny, Nesburn Anthony B, Kuppermann Baruch D, Bahraoui Elmostafa, Vahed Hawa, Gil Daniel, Jones Trevor M, Ulmer Jeffrey B, BenMohamed Lbachir", "evidence": [ { "database": "IEDB", "id": "1310643", "url": "https://www.iedb.org/epitope/1310643" }, { "database": "IEDB", "id": "1332359", "url": "https://www.iedb.org/epitope/1332359" }, { "database": "IEDB", "id": "1333722", "url": "https://www.iedb.org/epitope/1333722" } ], "reference": [ { "type": "PubMed", "id": "38605956", "url": "https://glygen.org/publication/PubMed/38605956" } ] } ], "pathway": [], "orthologs": [ { "uniprot_canonical_ac": "P59635-1", "protein_name": "ORF7a protein", "gene_name": "", "tax_id": 694009, "organism": "Severe acute respiratory syndrome-related coronavirus", "sequence": { "sequence": "MKIILFLTLIVFTSCELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSVSPKLFIRQEEVQQELYSPLFLIVAALVFLILCFTIKRKTE", "length": 122 }, "evidence": [ { "id": "UniRef50_P0DTC7", "url": "https://www.uniprot.org/uniref/UniRef50_P0DTC7", "database": "UniRef" } ], "glygen_name": "HCoV-SARS", "common_name": "SARS-CoV" } ], "go_annotation": { "categories": [ { "name": "Cellular 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"evidence": [ { "database": "UniProtKB", "id": "P0DTC7", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" }, { "database": "PubMed", "id": "33473190", "url": "https://glygen.org/publication/PubMed/33473190" } ] } ], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "structures": [], "lectin_list": [], "domain_list": [ { "evidence": [ { "id": "P0DTC7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" }, { "id": "36574644", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36574644" } ], "ann_type": "Motif_Annotation", "uniprotkb_annotation": "ER-retrieval motif", "eco_id": "ECO_0000269", "start_pos": 117, "end_pos": 119, "start_aa": "Lys", "end_aa": "Lys", "glycosite_overlap": "" }, { "evidence": [ { "id": "P0DTC7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC7" }, { "id": "PRU01267", "database": "PROSITE", "url": "https://prosite.expasy.org/PRU01267" } ], "ann_type": "Domain_Extent_Annotation", "uniprotkb_annotation": "X4e", "eco_id": "ECO_0000255", "start_pos": 16, "end_pos": 81, "start_aa": "Glu", "end_aa": "Ser", "glycosite_overlap": "" } ], "binding_sites": [], "synthesized_glycans": [], "enzyme_annotation": [], "cluster_types": [ { "name": "homologset.uniref", "label": "UniRef Homologs" } ], "sequence_features": { "n_linked_sites": [], "o_linked_sites": [], "snv_sites": [], "glycation_sites": [], "phosphorylation_sites": [], "sequon_annotation_sites": [] }, "class_list": [], "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], 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May act as a secreted virokine by mimicking interleukin-17A (IL17A), and thereby binding to the IL17RA receptor, leading to activation of the IL17 pathway and increased secretion of pro-inflammatory factors (PubMed:35343786, PubMed:36689483). Contributes to the cytokine storm during SARS-CoV-2 infection when secreted by unconventional pathway (PubMed:33723527, PubMed:36689483). May act by down-regulating major histocompability complex class I (MHC-I) at cell surface (PubMed:34021074, PubMed:35157849). May inhibit expression of some members of the IFN-stimulated gene (ISG) family including hosts IGF2BP1/ZBP1, MX1 and MX2, and DHX58 (PubMed:34177923).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8#function" }, { "database": "PubMed", "id": "33723527", "url": "https://glygen.org/publication/PubMed/33723527" }, { "database": "PubMed", "id": "31986261", "url": "https://glygen.org/publication/PubMed/31986261" }, { "database": "PubMed", "id": "36689483", "url": "https://glygen.org/publication/PubMed/36689483" }, { "database": "PubMed", "id": "34021074", "url": "https://glygen.org/publication/PubMed/34021074" }, { "database": "PubMed", "id": "35343786", "url": "https://glygen.org/publication/PubMed/35343786" }, { "database": "PubMed", "id": "35157849", "url": "https://glygen.org/publication/PubMed/35157849" }, { "database": "PubMed", "id": "34177923", "url": "https://glygen.org/publication/PubMed/34177923" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "COVID-19", "description": "A disease caused by infection with severe acute respiratory syndrome coronavirus 2." }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "coronavirus disease 2019", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome 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Genet. Evol.", "date": "2020", "authors": "Laha S, Chakraborty J, Das S, Manna SK, Biswas S, Chatterjee R", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "32615316", "url": "https://glygen.org/publication/PubMed/32615316" } ] }, { "title": "ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection.", "journal": "Nat. Immunol.", "date": "2020", "authors": "Hachim Asmaa, Kavian Niloufar, Cohen Carolyn A, Chin Alex W H, Chu Daniel K W, Mok Chris K P, Tsang Owen T Y, Yeung Yiu Cheong, Perera Ranawaka A P M, Poon Leo L M, Peiris J S Malik, Valkenburg Sophie A", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "32807944", "url": "https://glygen.org/publication/PubMed/32807944" } ] }, { "title": "Characterization of accessory genes in coronavirus genomes.", "journal": "Virol. J.", "date": "2020", "authors": "Michel Christian Jean, Mayer Claudine, Poch Olivier, Thompson Julie Dawn", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "32854725", "url": "https://glygen.org/publication/PubMed/32854725" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", "authors": "Nelde Annika, Bilich Tatjana, Heitmann Jonas S, Maringer Yacine, Salih Helmut R, Roerden Malte, L\u00fcbke Maren, Bauer Jens, Rieth Jonas, Wacker Marcel, Peter Andreas, H\u00f6rber Sebastian, Traenkle Bjoern, Kaiser Philipp D, Rothbauer Ulrich, Becker Matthias, Junker Daniel, Krause G\u00e9rard, Strengert Monika, Schneiderhan-Marra Nicole, Templin Markus F, Joos Thomas O, Kowalewski Daniel J, Stos-Zweifel Vlatka, Fehr Michael, Rabsteyn Armin, Mirakaj Valbona, Karbach Julia, J\u00e4ger Elke, Graf Michael, Gruber Lena-Christin, Rachfalski David, Preu\u00df Beate, Hagelstein Ilona, M\u00e4rklin Melanie, Bakchoul Tamam, Gouttefangeas C\u00e9cile, Kohlbacher Oliver, Klein Reinhild, Stevanovi\u0107 Stefan, Rammensee Hans-Georg, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310570", "url": "https://www.iedb.org/epitope/1310570" }, { "database": "IEDB", "id": "1310806", "url": "https://www.iedb.org/epitope/1310806" } ], "reference": [ { "type": "PubMed", "id": "32999467", "url": "https://glygen.org/publication/PubMed/32999467" } ] }, { "title": "Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2021", "authors": "Flower TG, Buffalo CZ, Hooy RM, Allaire M, Ren X, Hurley JH", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "33361333", "url": "https://glygen.org/publication/PubMed/33361333" } ] }, { "title": "Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020.", "journal": "Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin", "date": "2021", "authors": "Leung K, Shum MH, Leung GM, Lam TT, Wu JT", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "33413740", "url": "https://glygen.org/publication/PubMed/33413740" } ] }, { "title": "ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway.", "journal": "iScience", "date": "2021", "authors": "Lin X, Fu B, Yin S, Li Z, Liu H, Zhang H, Xing N, Wang Y, Xue W, Xiong Y, Zhang S, Zhao Q, Xu S, Zhang J, Wang P, Nian W, Wang X, Wu H", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": 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"Zhang Y, Chen Y, Li Y, Huang F, Luo B, Yuan Y, Xia B, Ma X, Yang T, Yu F, Liu J, Liu B, Song Z, Chen J, Yan S, Wu L, Pan T, Zhang X, Li R, Huang W, He X, Xiao F, Zhang J, Zhang H", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "34021074", "url": "https://glygen.org/publication/PubMed/34021074" } ] }, { "title": "SARS-CoV-2 ORF8 Forms Intracellular Aggregates and Inhibits IFN\u03b3-Induced Antiviral Gene Expression in Human Lung Epithelial Cells.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Geng Hua, Subramanian Saravanan, Wu Longtao, Bu Heng-Fu, Wang Xiao, Du Chao, De Plaen Isabelle G, Tan Xiao-Di", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "34177923", "url": "https://glygen.org/publication/PubMed/34177923" } ] }, { "title": "Profiling CD8+ T\u00a0cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants.", "journal": "Cell reports", "date": "2021-09-14", "authors": "Zhang Hang, Deng Shasha, Ren Liting, Zheng Peiyi, Hu Xiaowen, Jin Tengchuan, Tan Xu", "evidence": [ { "database": "IEDB", "id": "1597011", "url": "https://www.iedb.org/epitope/1597011" } ], "reference": [ { "type": "PubMed", "id": "34506741", "url": "https://glygen.org/publication/PubMed/34506741" } ] }, { "title": "Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2.", "journal": "Science immunology", "date": "2022-01-21", "authors": "Francis Joshua M, Leistritz-Edwards Del, Dunn Augustine, Tarr Christina, Lehman Jesse, Dempsey Conor, Hamel Andrew, Rayon Violeta, Liu Gang, Wang Yuntong, Wille Marcos, Durkin Melissa, Hadley Kane, Sheena Aswathy, Roscoe Benjamin, Ng Mark, Rockwell Graham, Manto Margaret, Gienger Elizabeth, Nickerson Joshua, , Moarefi Amir, Noble Michael, Malia Thomas, Bardwell Philip D, Gordon William, Swain Joanna, Skoberne Mojca, Sauer Karsten, Harris Tim, Goldrath Ananda W, Shalek Alex K, Coyle Anthony J, Benoist Christophe, Pregibon Daniel C", "evidence": [ { "database": "IEDB", "id": "1310957", "url": "https://www.iedb.org/epitope/1310957" }, { "database": "IEDB", "id": "1334426", "url": "https://www.iedb.org/epitope/1334426" }, { "database": "IEDB", "id": "1597011", "url": "https://www.iedb.org/epitope/1597011" }, { "database": "IEDB", "id": "2134058", "url": "https://www.iedb.org/epitope/2134058" }, { "database": "IEDB", "id": "2134085", "url": "https://www.iedb.org/epitope/2134085" }, { "database": "IEDB", "id": "2134315", "url": "https://www.iedb.org/epitope/2134315" }, { "database": "IEDB", "id": "2134377", "url": "https://www.iedb.org/epitope/2134377" } ], "reference": [ { "type": "PubMed", "id": "34793243", "url": "https://glygen.org/publication/PubMed/34793243" } ] }, { "title": "A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity.", "journal": "Nature", "date": "2022-01", "authors": "Heitmann Jonas S, Bilich Tatjana, Tandler Claudia, Nelde Annika, Maringer Yacine, Marconato Maddalena, Reusch Julia, J\u00e4ger Simon, Denk Monika, Richter Marion, Anton Leonard, Weber Lisa Marie, Roerden Malte, Bauer Jens, Rieth Jonas, Wacker Marcel, H\u00f6rber Sebastian, Peter Andreas, Meisner Christoph, Fischer Imma, L\u00f6ffler Markus W, Karbach Julia, J\u00e4ger Elke, Klein Reinhild, Rammensee Hans-Georg, Salih Helmut R, Walz Juliane S", "evidence": [ { "database": "IEDB", "id": "1310806", "url": "https://www.iedb.org/epitope/1310806" } ], "reference": [ { "type": "PubMed", "id": "34814158", "url": "https://glygen.org/publication/PubMed/34814158" } ] }, { "title": "Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair.", "journal": "Open biology", "date": "2022-02", "authors": "de Castro Mateus V, Santos Keity S, Apostolico 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Yokomaku Y, Iwatani Y", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8#ptm_processing" }, { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "35157849", "url": "https://glygen.org/publication/PubMed/35157849" } ] }, { "title": "Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8.", "journal": "mBio", "date": "2022", "authors": "Wu X, Xia T, Shin WJ, Yu KM, Jung W, Herrmann A, Foo SS, Chen W, Zhang P, Lee JS, Poo H, Comhair SAA, Jehi L, Choi YK, Ensser A, Jung JU", "evidence": [ { "database": "UniProtKB", "id": "P0DTC8", "url": "https://www.uniprot.org/uniprotkb/P0DTC8" } ], "reference": [ { "type": "PubMed", "id": "35343786", "url": "https://glygen.org/publication/PubMed/35343786" } ] }, { "title": "SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens.", "journal": 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Disrupts the association betwen NLRP3 and ABHD8, enhancing NLRP3 stability and leading to increased inflammasome activation (PubMed:39225180).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9#function" }, { "database": "PubMed", "id": "34341353", "url": "https://glygen.org/publication/PubMed/34341353" }, { "database": "PubMed", "id": "39225180", "url": "https://glygen.org/publication/PubMed/39225180" } ] }, { "annotation": "Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M (PubMed:33264373). Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication. 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binding domain reveals potential unique drug targeting sites.", "journal": "Acta pharmaceutica Sinica. B", "date": "2020", "authors": "Kang S, Yang M, Hong Z, Zhang L, Huang Z, Chen X, He S, Zhou Z, Zhou Z, Chen Q, Yan Y, Zhang C, Shan H, Chen S", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "reference": [ { "type": "PubMed", "id": "32363136", "url": "https://glygen.org/publication/PubMed/32363136" } ] }, { "title": "Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.", "journal": "Protein Sci.", "date": "2020", "authors": "Ye Qiaozhen, West Alan M V, Silletti Steve, Corbett Kevin D", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "reference": [ { "type": "PubMed", "id": "32654247", "url": "https://glygen.org/publication/PubMed/32654247" } ] }, { "title": "SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls.", "journal": "Nature", "date": "2020-08", "authors": "Le Bert Nina, Tan Anthony T, Kunasegaran Kamini, Tham Christine Y L, Hafezi Morteza, Chia Adeline, Chng Melissa Hui Yen, Lin Meiyin, Tan Nicole, Linster Martin, Chia Wan Ni, Chen Mark I-Cheng, Wang Lin-Fa, Ooi Eng Eong, Kalimuddin Shirin, Tambyah Paul Anantharajah, Low Jenny Guek-Hong, Tan Yee-Joo, Bertoletti Antonio", "evidence": [ { "database": "IEDB", "id": "1172352", "url": "https://www.iedb.org/epitope/1172352" } ], "reference": [ { "type": "PubMed", "id": "32668444", "url": "https://glygen.org/publication/PubMed/32668444" } ] }, { "title": "Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes.", "journal": "Genome medicine", "date": "2020-08-13", "authors": "Poran Asaf, Harjanto Dewi, Malloy Matthew, Arieta Christina M, Rothenberg Daniel A, Lenkala Divya, van Buuren Marit M, Addona Terri A, Rooney Michael S, Srinivasan Lakshmi, Gaynor Richard B", "evidence": [ { "database": "IEDB", "id": "37473", "url": "https://www.iedb.org/epitope/37473" }, { "database": "IEDB", "id": "1125078", "url": "https://www.iedb.org/epitope/1125078" }, { "database": "IEDB", "id": "1125146", "url": "https://www.iedb.org/epitope/1125146" } ], "reference": [ { "type": "PubMed", "id": "32791978", "url": "https://glygen.org/publication/PubMed/32791978" } ] }, { "title": "Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19.", "journal": "Nature immunology", "date": "2020-11", "authors": "Peng Yanchun, Mentzer Alexander J, Liu Guihai, Yao Xuan, Yin Zixi, Dong Danning, Dejnirattisai Wanwisa, Rostron Timothy, Supasa Piyada, Liu Chang, L\u00f3pez-Camacho C\u00e9sar, Slon-Campos Jose, Zhao Yuguang, Stuart David I, Paesen Guido C, Grimes Jonathan M, Antson Alfred A, Bayfield Oliver W, Hawkins Dorothy E D P, Ker De-Sheng, Wang Beibei, Turtle Lance, Subramaniam Krishanthi, Thomson Paul, Zhang Ping, Dold Christina, Ratcliff Jeremy, Simmonds Peter, de Silva Thushan, Sopp Paul, Wellington Dannielle, Rajapaksa Ushani, Chen Yi-Ling, Salio Mariolina, Napolitani Giorgio, Paes Wayne, Borrow Persephone, Kessler Benedikt M, Fry Jeremy W, Schwabe Nikolai F, Semple Malcolm G, Baillie J Kenneth, Moore Shona C, Openshaw Peter J M, Ansari M Azim, Dunachie Susanna, Barnes Eleanor, Frater John, Kerr Georgina, Goulder Philip, Lockett Teresa, Levin Robert, Zhang Yonghong, Jing Ronghua, Ho Ling-Pei, , , Cornall Richard J, Conlon Christopher P, Klenerman Paul, Screaton Gavin R, Mongkolsapaya Juthathip, McMichael Andrew, Knight Julian C, Ogg Graham, Dong Tao", "evidence": [ { "database": "IEDB", "id": "33667", "url": "https://www.iedb.org/epitope/33667" }, { "database": "IEDB", "id": "37611", "url": "https://www.iedb.org/epitope/37611" }, { "database": "IEDB", "id": "190494", "url": "https://www.iedb.org/epitope/190494" }, { "database": "IEDB", "id": "1309129", "url": "https://www.iedb.org/epitope/1309129" } ], "reference": [ { "type": "PubMed", "id": 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} ], "reference": [ { "type": "PubMed", "id": "32913053", "url": "https://glygen.org/publication/PubMed/32913053" } ] }, { "title": "SR/RS Motifs as Critical Determinants of Coronavirus Life Cycle.", "journal": "Frontiers in molecular biosciences", "date": "2020", "authors": "Nikolakaki Eleni, Giannakouros Thomas", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "reference": [ { "type": "PubMed", "id": "32974389", "url": "https://glygen.org/publication/PubMed/32974389" } ] }, { "title": "Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19.", "journal": "Cell", "date": "2020-10-01", "authors": "Sekine Takuya, Perez-Potti Andr\u00e9, Rivera-Ballesteros Olga, Str\u00e5lin Kristoffer, Gorin Jean-Baptiste, Olsson Annika, Llewellyn-Lacey Sian, Kamal Habiba, Bogdanovic Gordana, Muschiol Sandra, Wullimann David J, Kammann Tobias, Emg\u00e5rd Johanna, Parrot Tiphaine, Folkesson Elin, , Rooyackers Olav, Eriksson Lars I, Henter Jan-Inge, S\u00f6nnerborg Anders, Allander Tobias, Albert Jan, Nielsen Morten, Klingstr\u00f6m Jonas, Gredmark-Russ Sara, Bj\u00f6rkstr\u00f6m Niklas K, Sandberg Johan K, Price David A, Ljunggren Hans-Gustaf, Aleman Soo, Buggert Marcus", "evidence": [ { "database": "IEDB", "id": "37473", "url": "https://www.iedb.org/epitope/37473" }, { "database": "IEDB", "id": "60242", "url": "https://www.iedb.org/epitope/60242" } ], "reference": [ { "type": "PubMed", "id": "32979941", "url": "https://glygen.org/publication/PubMed/32979941" } ] }, { "title": "Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity.", "journal": "Science (New York, N.Y.)", "date": "2020-11-27", "authors": "Shrock Ellen, Fujimura Eric, Kula Tomasz, Timms Richard T, Lee I-Hsiu, Leng Yumei, Robinson Matthew L, Sie Brandon M, Li Mamie Z, Chen Yuezhou, Logue Jennifer, Zuiani Adam, McCulloch Denise, Lelis Felipe J N, Henson Stephanie, Monaco Daniel R, Travers Meghan, Habibi Shaghayegh, Clarke William A, Caturegli Patrizio, Laeyendecker Oliver, Piechocka-Trocha Alicja, Li Jonathan Z, Khatri Ashok, Chu Helen Y, , Villani Alexandra-Chlo\u00e9, Kays Kyle, Goldberg Marcia B, Hacohen Nir, Filbin Michael R, Yu Xu G, Walker Bruce D, Wesemann Duane R, Larman H Benjamin, Lederer James A, Elledge Stephen J", "evidence": [ { "database": "IEDB", "id": "1311682", "url": "https://www.iedb.org/epitope/1311682" }, { "database": "IEDB", "id": "1311749", "url": "https://www.iedb.org/epitope/1311749" }, { "database": "IEDB", "id": "1311775", "url": "https://www.iedb.org/epitope/1311775" }, { "database": "IEDB", "id": "1311869", "url": "https://www.iedb.org/epitope/1311869" } ], "reference": [ { "type": "PubMed", "id": "32994364", "url": "https://glygen.org/publication/PubMed/32994364" } ] }, { "title": "SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition.", "journal": "Nature immunology", "date": "2021-01", 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immunology", "date": "2021-07", "authors": "Holenya Pavlo, Lange Paul Joris, Reimer Ulf, Woltersdorf Wolfram, Panterodt Thomas, Glas Michael, Wasner Mark, Eckey Maren, Drosch Michael, Hollidt J\u00f6rg-Michael, Naumann Michael, Kern Florian, Wenschuh Holger, Lange Robert, Schnatbaum Karsten, Bier Frank F", "evidence": [ { "database": "IEDB", "id": "1311749", "url": "https://www.iedb.org/epitope/1311749" } ], "reference": [ { "type": "PubMed", "id": "33772767", "url": "https://glygen.org/publication/PubMed/33772767" } ] }, { "title": "SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.", "journal": "Science immunology", "date": "2021-04-14", "authors": "Saini Sunil Kumar, Hersby Ditte Stampe, Tamhane Tripti, Povlsen Helle Rus, Amaya Hernandez Susana Patricia, Nielsen Morten, Gang Anne Ortved, Hadrup Sine Reker", "evidence": [ { "database": "IEDB", "id": "3810", "url": "https://www.iedb.org/epitope/3810" }, { 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M, Riboldi-Tunnicliffe Alan, Chen Weisan, D'Orsogna Lloyd, Khanna Rajiv, Short Kirsty R, Smith Corey, Gras Stephanie", "evidence": [ { "database": "IEDB", "id": "17385", "url": "https://www.iedb.org/epitope/17385" }, { "database": "IEDB", "id": "60242", "url": "https://www.iedb.org/epitope/60242" }, { "database": "IEDB", "id": "1311570", "url": "https://www.iedb.org/epitope/1311570" }, { "database": "IEDB", "id": "1392399", "url": "https://www.iedb.org/epitope/1392399" } ], "reference": [ { "type": "PubMed", "id": "33945786", "url": "https://glygen.org/publication/PubMed/33945786" } ] }, { "title": "SARS-CoV-2-Seronegative Subjects Target CTL Epitopes in the SARS-CoV-2 Nucleoprotein Cross-Reactive to Common Cold Coronaviruses.", "journal": "Frontiers in immunology", "date": "2021", "authors": "Schmidt Katja G, Nganou-Makamdop Krystelle, Tenbusch Matthias, El Kenz Boutaina, Maier Clara, Lapuente Dennis, \u00dcberla Klaus, Spriewald Bernd, Bergmann Silke, Harrer Ellen G, Harrer Thomas", 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Adv.", "date": "2022", "authors": "Bessa Luiza Mamigonian, Guseva Serafima, Camacho-Zarco Aldo R, Salvi Nicola, Maurin Damien, Perez Laura Mari\u00f1o, Botova Maiia, Malki Anas, Nanao Max, Jensen Malene Ringkj\u00f8bing, Ruigrok Rob W H, Blackledge Martin", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "reference": [ { "type": "PubMed", "id": "35044811", "url": "https://glygen.org/publication/PubMed/35044811" } ] }, { "title": "Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair.", "journal": "Open biology", "date": "2022-02", "authors": "de Castro Mateus V, Santos Keity S, Apostolico Juliana S, Fernandes Edgar R, Almeida Rafael R, Levin Gabriel, Magawa Jhosiene Y, Nunes Jo\u00e3o Paulo S, Bruni Mirian, Yamamoto Marcio M, Lima Ariane C, Silva Monize V R, Matos Larissa R B, Coria Vivian R, Castelli Erick C, Scliar Marilia O, Kuramoto Andreia, Bruno Fernanda R, Jacintho Lucas C, Nunes Kelly, Wang Jaqueline Y T, Coelho Veronica P, Neto Miguel Mitne, Maciel Rui M B, Naslavsky Michel S, Passos-Bueno Maria Rita, Boscardin Silvia B, Rosa Daniela S, Kalil Jorge, Zatz Mayana, Cunha-Neto Edecio", "evidence": [ { "database": "IEDB", "id": "34851", "url": "https://www.iedb.org/epitope/34851" }, { "database": "IEDB", "id": "37473", "url": "https://www.iedb.org/epitope/37473" }, { "database": "IEDB", "id": "923297", "url": "https://www.iedb.org/epitope/923297" } ], "reference": [ { "type": "PubMed", "id": "35104433", "url": "https://glygen.org/publication/PubMed/35104433" } ] }, { "title": "SARS-CoV-2-specific T cells generated for adoptive immunotherapy are capable of recognizing multiple SARS-CoV-2 variants.", "journal": "PLoS pathogens", "date": "2022-02", "authors": "Panikkar Archana, Lineburg Katie E, Raju Jyothy, Chew Keng Yih, Ambalathingal George R, Rehan Sweera, Swaminathan Srividhya, Crooks Pauline, Le Texier Laetitia, Beagley Leone, Best Shannon, Solomon Matthew, 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"journal": "Immunity", "date": "2022-07-12", "authors": "Rowntree Louise C, Nguyen Thi H O, Kedzierski Lukasz, Neeland Melanie R, Petersen Jan, Crawford Jeremy Chase, Allen Lilith F, Clemens E Bridie, Chua Brendon, McQuilten Hayley A, Minervina Anastasia A, Pogorelyy Mikhail V, Chaurasia Priyanka, Tan Hyon-Xhi, Wheatley Adam K, Jia Xiaoxiao, Amanat Fatima, Krammer Florian, Allen E Kaitlynn, Sonda Sabrina, Flanagan Katie L, Jumarang Jaycee, Pannaraj Pia S, Licciardi Paul V, Kent Stephen J, Bond Katherine A, Williamson Deborah A, Rossjohn Jamie, Thomas Paul G, Tosif Shidan, Crawford Nigel W, van de Sandt Carolien E, Kedzierska Katherine", "evidence": [ { "database": "IEDB", "id": "33667", "url": "https://www.iedb.org/epitope/33667" }, { "database": "IEDB", "id": "60242", "url": "https://www.iedb.org/epitope/60242" }, { "database": "IEDB", "id": "190494", "url": "https://www.iedb.org/epitope/190494" } ], "reference": [ { "type": "PubMed", "id": "35750048", "url": 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"https://glygen.org/publication/PubMed/35937077" } ] }, { "title": "Cross-reactivity of SARS-CoV-2- and influenza A-specific T cells in individuals exposed to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-09-22", "authors": "Chaisawangwong Worarat, Wang Hanzhi, Kouo Theodore, Salathe Sebastian F, Isser Ariel, Bieler Joan Glick, Zhang Maya L, Livingston Natalie K, Li Shuyi, Horowitz Joseph J, Samet Ron E, Zyskind Israel, Rosenberg Avi Z, Schneck Jonathan P", "evidence": [ { "database": "IEDB", "id": "37473", "url": "https://www.iedb.org/epitope/37473" } ], "reference": [ { "type": "PubMed", "id": "36134660", "url": "https://glygen.org/publication/PubMed/36134660" } ] }, { "title": "Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection.", "journal": "Nature communications", "date": "2022-09-23", "authors": "Khatamzas Elham, Antwerpen Markus H, Rehn Alexandra, Graf Alexander, Hellmuth Johannes 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"" } ] }, { "name": "Molecular Function", "total": 8, "go_terms": [ { "name": "RNA binding", "id": "GO:0003723", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0003723", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "identical protein binding", "id": "GO:0042802", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0042802", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "protein homodimerization activity", "id": "GO:0042803", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0042803", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "MHC class I protein binding", "id": "GO:0042288", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0042288", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "poly(U) RNA binding", "id": "GO:0008266", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008266", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "RNA stem-loop binding", "id": "GO:0035613", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0035613", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "molecular condensate scaffold activity", "id": "GO:0140693", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0140693", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "protein sequestering activity", "id": "GO:0140311", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0140311", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" } ] }, { "name": "Cellular Component", "total": 10, "go_terms": [ { "name": "extracellular region", "id": "GO:0005576", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005576", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "cytoplasm", "id": "GO:0005737", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005737", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "MHC class I protein complex", "id": "GO:0042612", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0042612", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "ribonucleoprotein complex", "id": "GO:1990904", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:1990904", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "viral capsid", "id": "GO:0019028", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019028", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "viral nucleocapsid", "id": "GO:0019013", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0019013", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "host cell perinuclear region of cytoplasm", "id": "GO:0044220", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0044220", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "host cell endoplasmic reticulum-Golgi intermediate compartment", "id": "GO:0044172", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0044172", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "host cell Golgi apparatus", "id": "GO:0044177", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0044177", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" }, { "name": "host extracellular space", "id": "GO:0043655", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0043655", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" } ], "pmid": "" } ] } ] }, "pro_annotation": [], "site_annotation": [ { "start_pos": 192, "end_pos": 194, "annotation": "n_glycosylation_sequon" }, { "start_pos": 196, "end_pos": 198, "annotation": "n_glycosylation_sequon" }, { "start_pos": 269, "end_pos": 271, "annotation": "n_glycosylation_sequon" }, { "start_pos": 47, "end_pos": 49, "annotation": "n_glycosylation_sequon" }, { "start_pos": 77, "end_pos": 79, "annotation": "n_glycosylation_sequon" } ], "ptm_annotation": [ { "annotation": "Acetylated (PubMed:39135075). Deacetylated by host HDAC6 which promotes association of the viral N protein with human G3BP1, disrupting cellular stress granule formation and facilitating viral replication (PubMed:39135075).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" }, { "database": "PubMed", "id": "39135075", "url": "https://glygen.org/publication/PubMed/39135075" } ] }, { "annotation": "Phosphorylated on serine residues by host GSK3A and GSK3B (PubMed:34593624, PubMed:35728038). This promotes the solubility of homodimers that would otherwise aggregate (PubMed:32974389). Host phosphatase would dephosphorylate the protein during assembly at M bound membranes (PubMed:32974389).", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" }, { "database": "PubMed", "id": "34593624", "url": "https://glygen.org/publication/PubMed/34593624" }, { "database": "PubMed", "id": "35728038", "url": "https://glygen.org/publication/PubMed/35728038" }, { "database": "PubMed", "id": "32974389", "url": "https://glygen.org/publication/PubMed/32974389" } ] }, { "annotation": "Proteolytically cleaved by host CASP6. The cleavage leads to two fragments and facilitates viral replication by inhibiting host IFN signaling. The two fragments may interact with IRF3 inhibiting its nuclear translocation after activation and reduce the expression of IFNB and IFN-stimulated genes.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" }, { "database": "PubMed", "id": "35922005", "url": "https://glygen.org/publication/PubMed/35922005" } ] }, { "annotation": "SUMOylated at Lys-65 by host TRIM28; SUMOylation promotes RNA association.", "evidence": [ { "database": "UniProtKB", "id": "P0DTC9", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" }, { "database": "PubMed", "id": "38172120", "url": "https://glygen.org/publication/PubMed/38172120" } ] } ], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "structures": [], "lectin_list": [], "domain_list": [ { "evidence": [ { "id": "P0DTC9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTC9" }, { "id": "PRU01277", "database": "PROSITE", 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"ac": "YP_009724389", "name": "ORF1ab polyprotein", "summary": "", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724389" }, "gene_names": [ { "name": "rep", "type": "recommended", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ] }, { "name": "1a-1b", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ] } ], "protein_names": [ { "name": "Replicase polyprotein 1ab", "type": "recommended", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "ExoN", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "GFL", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": 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"Non-structural protein 1", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 3", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 5", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "Non-structural protein 9", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "ORF1ab polyprotein", "type": "synonym", "evidence": [ { "id": "YP_009724389", "database": "RefSeq", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724389" }, { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "PL-PRO", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "PL2-PRO", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "Papain-like proteinase", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "Proofreading exoribonuclease nsp14", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "RNA-capping enzyme subunit nsp9", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "SARS coronavirus main proteinase", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp12", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp13", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp14", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp15", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp16", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp1", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp3", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp5", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "nsp9", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "p65 homolog", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] }, { "name": "pp1ab", "type": "synonym", "evidence": [ { "id": "P0DTD1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#names_and_taxonomy" } ] } ], "function": [ { "annotation": "Cleaves the C-terminus of replicase polyprotein at 11 sites (PubMed:32321856). Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291, PubMed:32272481). Cleaves and inactivates human TRMT1, preventing tRNA guanine(26)-dimethylation of tRNAs (PubMed:37073102, PubMed:38814682, PubMed:39773525). May cleave human NLRP1 in lung epithelial cells, thereby activating the NLRP1 inflammasome pathway (PubMed:35594856). May cleave human GSDMD, triggering alternative GSDME-mediated epithelial cell death upon activation of the NLRP1 inflammasome, which may enhance the release interleukins 1B, 6, 16 and 18 (PubMed:35594856). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (PubMed:32198291, PubMed:32272481). Cleaves host STIM1 producing two functional fragments: STIM1 N-terminus, which inhibits MAVS-mediated IFNB signaling by disrupting signalosome formation, and STIM1 C-terminus, which suppresses p65-driven IFNB transcription (PubMed:41289387). Inhibits host pyroptosis through the cleavage of host gasdermin D/GSDMD (PubMed:40118151).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "32272481", "url": "https://glygen.org/publication/PubMed/32272481" }, { "database": "PubMed", "id": "35594856", "url": "https://glygen.org/publication/PubMed/35594856" }, { "database": "PubMed", "id": "32198291", "url": "https://glygen.org/publication/PubMed/32198291" }, { "database": "PubMed", "id": "32321856", "url": "https://glygen.org/publication/PubMed/32321856" }, { "database": "PubMed", "id": "38814682", "url": "https://glygen.org/publication/PubMed/38814682" }, { "database": "PubMed", "id": "37073102", "url": "https://glygen.org/publication/PubMed/37073102" }, { "database": "PubMed", "id": "39773525", "url": "https://glygen.org/publication/PubMed/39773525" }, { "database": "PubMed", "id": "41289387", "url": "https://glygen.org/publication/PubMed/41289387" }, { "database": "PubMed", "id": "40118151", "url": "https://glygen.org/publication/PubMed/40118151" } ] }, { "annotation": "Enhances mRNA repression of the 4EHP-GYF2 complex in the host, thereby inhibiting the antiviral response and facilitating SARS-CoV-2 replication. Possibly acts in cooperation with nsp1, which induces ribosome stalling on host mRNA, triggering mRNA repression by the host 4EHP-GYF2 complex which is enhanced by nsp2.", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "35878012", "url": "https://glygen.org/publication/PubMed/35878012" } ] }, { "annotation": "Forms a primer, NSP9-pU, which is utilized by the polymerase for the initiation of RNA chains (PubMed:37794589). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP8, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "37794589", "url": "https://glygen.org/publication/PubMed/37794589" } ] }, { "annotation": "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:32680882, PubMed:32979938, PubMed:33080218). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). This inhibits the integrated stress response (ISR) in the infected cell by preventing EIF2S1/eIF2-alpha phosphorylation upstream of stress granule formation and depletes host G3BP1 (PubMed:36534661). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32908316", "url": "https://glygen.org/publication/PubMed/32908316" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "33479166", "url": "https://glygen.org/publication/PubMed/33479166" }, { "database": "PubMed", "id": "32680882", "url": "https://glygen.org/publication/PubMed/32680882" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "36534661", "url": "https://glygen.org/publication/PubMed/36534661" } ] }, { "annotation": "Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs (PubMed:35944563). N7-methyl guanosine cap is a prerequisite for binding of nsp16 (PubMed:35944563). Therefore, it plays an essential role in cap methylation of viral mRNAs, which is essential to evade the immune system, especially when restricted by human IFIT1 and IFIT3 (PubMed:35944563, PubMed:36722972, PubMed:36285486). May disrupt host mRNA splicing in nucleus by interacting with pre-mRNA Recognition Domains of the U1 and U2 snRNAs (PubMed:33080218).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" }, { "database": "PubMed", "id": "36722972", "url": "https://glygen.org/publication/PubMed/36722972" }, { "database": "PubMed", "id": "36285486", "url": "https://glygen.org/publication/PubMed/36285486" } ] }, { "annotation": "Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" } ] }, { "annotation": "Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease (By similarity) and nsp16 2'-O-methyltransferase activities (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation.", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "annotation": "Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511). LDs are consumed during DMV formation (PubMed:35551511). Binds to host TBK1 without affecting TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "35551511", "url": "https://glygen.org/publication/PubMed/35551511" } ] }, { "annotation": "Plays a role in viral RNA synthesis (PubMed:32277040, PubMed:32358203, PubMed:32438371, PubMed:32526208). Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers (By similarity).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32526208", "url": "https://glygen.org/publication/PubMed/32526208" }, { "database": "PubMed", "id": "32358203", "url": "https://glygen.org/publication/PubMed/32358203" }, { "database": "PubMed", "id": "32438371", "url": "https://glygen.org/publication/PubMed/32438371" }, { "database": "PubMed", "id": "32277040", "url": "https://glygen.org/publication/PubMed/32277040" }, { "database": "PubMed", "id": "33080218", "url": "https://glygen.org/publication/PubMed/33080218" } ] }, { "annotation": "Plays a role in viral RNA synthesis (PubMed:33232691). Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium (By similarity). Binds to host TBK1 and inhibits TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "32979938", "url": "https://glygen.org/publication/PubMed/32979938" }, { "database": "PubMed", "id": "33232691", "url": "https://glygen.org/publication/PubMed/33232691" } ] }, { "annotation": "Plays a role in viral RNA synthesis through two distinct activities. The N7-guanine methyltransferase activity plays a role in the formation of the cap structure GpppA-RNA (PubMed:35944563). The proofreading exoribonuclease reduces the sensitivity of the virus to RNA mutagens during replication (By similarity). This activity acts on both ssRNA and dsRNA in a 3'-5' direction (By similarity).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "annotation": "Plays a role in viral transcription/replication and prevents the simultaneous activation of host cell dsRNA sensors, such as MDA5/IFIH1, OAS, and PKR (By similarity). Acts by degrading the 5'-polyuridines generated during replication of the poly(A) region of viral genomic and subgenomic RNAs (PubMed:33504779, PubMed:33564093). Catalyzes a two-step reaction in which a 2'3'-cyclic phosphate (2'3'-cP) is first generated by 2'-O transesterification, which is then hydrolyzed to a 3'-phosphate (3'-P) (PubMed:33504779, PubMed:33564093). If not degraded, poly(U) RNA would hybridize with poly(A) RNA tails and activate host dsRNA sensors (By similarity). May bind genomic dsRNA in association with the replication-transcription complex (RTC), and play a role in nsp12 discontinous transcription (PubMed:34562452, PubMed:35706445).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "35706445", "url": "https://glygen.org/publication/PubMed/35706445" }, { "database": "PubMed", "id": "34562452", "url": "https://glygen.org/publication/PubMed/34562452" }, { "database": "PubMed", "id": "33504779", "url": "https://glygen.org/publication/PubMed/33504779" } ] }, { "annotation": "RNA-directed RNA polymerase that catalyzes the transcription of viral genomic and subgenomic RNAs. Acts in complex with nsp7 and nsp8 to transcribe both the minus and positive strands of genomic RNA (PubMed:32277040, PubMed:32358203, PubMed:32438371, PubMed:32526208). The kinase-like NiRAN domain of NSP12 attaches one or more nucleotides to the amino terminus of NSP9, forming a covalent RNA-protein intermediate that serves as transcription/replication primer (PubMed:37794589). Subgenomic RNAs (sgRNAs) are formed by discontinuous transcription: The polymerase has the ability to pause at transcription-regulating sequences (TRS) and jump to the leader TRS, resulting in a major deletion (PubMed:35706445). This creates a series of subgenomic RNAs that are replicated, transcribed and translated (PubMed:35706445). In addition, Nsp12 is a subunit of the viral RNA capping enzyme that catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs (PubMed:35944563). Subsequently, the NiRAN domain transfers RNA to GDP, and forms the core cap structure GpppA-RNA (PubMed:35944563).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" }, { "database": "PubMed", "id": "32438371", "url": "https://glygen.org/publication/PubMed/32438371" }, { "database": "PubMed", "id": "32526208", "url": "https://glygen.org/publication/PubMed/32526208" }, { "database": "PubMed", "id": "35706445", "url": "https://glygen.org/publication/PubMed/35706445" }, { "database": "PubMed", "id": "32277040", "url": "https://glygen.org/publication/PubMed/32277040" }, { "database": "PubMed", "id": "32358203", "url": "https://glygen.org/publication/PubMed/32358203" }, { "database": "PubMed", "id": "37794589", "url": "https://glygen.org/publication/PubMed/37794589" } ] }, { "annotation": "Responsible for the cleavages located at the N-terminus of the replicase polyprotein. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication (PubMed:35551511). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Also prevents host NF-kappa-B signaling (By similarity). In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates (PubMed:32726803). Cleaves preferentially ISG15 from antiviral protein IFIH1 (MDA5), but not RIGI (PubMed:33727702). Contains an ADP-ribose hydrolase activity that binds ADP-ribose and catalyzes the removal of mono-ADP-ribose (de-MARylation), usually bound to a glutamate or aspartate (Probable) (PubMed:37242344). ADP-ribose hydrolase activity allows the virus to interfere with the host immune defenses involving poly-ADP-ribose polymerases (PARPs) (Probable). Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1#function" }, { "database": "UniProtKB", "id": "P0C6X7", "url": "https://www.uniprot.org/uniprotkb/P0C6X7#function" }, { "database": "PubMed", "id": "35551511", "url": "https://glygen.org/publication/PubMed/35551511" }, { "database": "PubMed", "id": "32733001", "url": "https://glygen.org/publication/PubMed/32733001" }, { "database": "PubMed", "id": "33727702", "url": "https://glygen.org/publication/PubMed/33727702" }, { "database": "PubMed", "id": "32578982", "url": "https://glygen.org/publication/PubMed/32578982" }, { "database": "PubMed", "id": "32726803", "url": "https://glygen.org/publication/PubMed/32726803" }, { "database": "PubMed", "id": "37242344", "url": "https://glygen.org/publication/PubMed/37242344" } ] } ], "disease": [ { "disease_id": "DOID:0080600", "recommended_name": { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID-19", "description": "A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a subtype of Betacoronavirus pandemicum." }, "synonyms": [ { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019 Novel Coronavirus (2019-nCoV)", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "2019-nCoV infection", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "COVID19", "description": "" }, { "id": "DOID:0080600", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080600", "name": "SARS-CoV-2 infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "COVID-19", "description": "A disease caused by infection with severe acute respiratory syndrome coronavirus 2." }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019 novel coronavirus infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "2019-nCoV infection", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "coronavirus disease 2019", "description": "" }, { "id": "MONDO:0100096", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100096", "name": "severe acute respiratory syndrome coronavirus 2 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"https://www.rcsb.org/structure/9I4V", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9I51", "url": "https://www.rcsb.org/structure/9I51", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9I53", "url": "https://www.rcsb.org/structure/9I53", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9I81", "url": "https://www.rcsb.org/structure/9I81", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9IKZ", "url": "https://www.rcsb.org/structure/9IKZ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9IMK", "url": "https://www.rcsb.org/structure/9IMK", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9IMM", "url": "https://www.rcsb.org/structure/9IMM", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9J19", "url": "https://www.rcsb.org/structure/9J19", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9JJ7", "url": "https://www.rcsb.org/structure/9JJ7", "database": "PDB", 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"categories": [ "3D Structure" ] }, { "id": "9MVM", "url": "https://www.rcsb.org/structure/9MVM", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9MVO", "url": "https://www.rcsb.org/structure/9MVO", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9MVP", "url": "https://www.rcsb.org/structure/9MVP", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9MVQ", "url": "https://www.rcsb.org/structure/9MVQ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6J", "url": "https://www.rcsb.org/structure/9N6J", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6L", "url": "https://www.rcsb.org/structure/9N6L", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6M", "url": "https://www.rcsb.org/structure/9N6M", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6N", "url": "https://www.rcsb.org/structure/9N6N", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6P", "url": "https://www.rcsb.org/structure/9N6P", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9N6R", "url": "https://www.rcsb.org/structure/9N6R", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9NPX", "url": "https://www.rcsb.org/structure/9NPX", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9NSK", "url": "https://www.rcsb.org/structure/9NSK", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9NSL", "url": "https://www.rcsb.org/structure/9NSL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9NWA", "url": "https://www.rcsb.org/structure/9NWA", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9NWC", "url": "https://www.rcsb.org/structure/9NWC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9P6P", "url": "https://www.rcsb.org/structure/9P6P", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9Q8H", "url": "https://www.rcsb.org/structure/9Q8H", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9R5T", "url": "https://www.rcsb.org/structure/9R5T", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9UHT", "url": "https://www.rcsb.org/structure/9UHT", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9VAO", "url": "https://www.rcsb.org/structure/9VAO", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9VCK", "url": "https://www.rcsb.org/structure/9VCK", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9VCL", "url": "https://www.rcsb.org/structure/9VCL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "9VWY", "url": "https://www.rcsb.org/structure/9VWY", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "PF00680", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF00680", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF01661", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF01661", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF05409", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF05409", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF06460", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF06460", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF06471", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF06471", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF06478", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF06478", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF08710", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08710", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF08715", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08715", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF08716", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08716", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF08717", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF08717", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF09401", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF09401", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF11501", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF11501", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF11633", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF11633", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF12124", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF12124", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF12379", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF12379", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF13087", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF13087", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF16251", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF16251", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF16348", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF16348", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19211", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19211", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19213", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19213", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19215", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19215", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19216", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19216", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19217", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19217", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19218", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19218", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF19219", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF19219", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF20631", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF20631", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF20632", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF20632", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "PF20633", "url": "https://www.ebi.ac.uk/interpro/entry/pfam/PF20633", "database": "Pfam", "categories": [ "Protein Classification", "Other" ] }, { "id": "YP_009724389", "url": "https://www.ncbi.nlm.nih.gov/protein/YP_009724389", "database": "RefSeq", "categories": [ "Protein" ] }, { "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTD1-1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1-1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P0DTD1", "url": "https://viral.glycomics.ku.dk/viewer/?uniprot=P0DTD1", "database": "Viral Glycome", "categories": [ "Organism-specific" ] } ], "sequence": { "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN", "length": 7096, "header": "sp|P0DTD1-1|R1AB_SARS2 Isoform 1 of Replicase polyprotein 1ab OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 SV=1 CANONICAL=P0DTD1-1" }, "isoforms": [ { "isoform_ac": "P0DTD1-1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1/entry#P0DTD1-1", "sequence": { "sequence": "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN", "length": 7096, "header": "sp|P0DTD1-1|R1AB_SARS2 Isoform 1 of Replicase polyprotein 1ab OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=rep PE=1 SV=1 CANONICAL=P0DTD1-1" }, "locus": {} } ], "glycosylation": [], "phosphorylation": [], "glycation": [], "keywords": [ "enzyme" ], "publication": [ { "title": "A new coronavirus associated with human respiratory disease in China.", "journal": "Nature", "date": "2020", "authors": "Wu Fan, Zhao Su, Yu Bin, Chen Yan-Mei, Wang Wen, Song Zhi-Gang, Hu Yi, Tao Zhao-Wu, Tian Jun-Hua, Pei Yuan-Yuan, Yuan Ming-Li, Zhang Yu-Ling, Dai Fa-Hui, Liu Yi, Wang Qi-Min, Zheng Jiao-Jiao, Xu Lin, Holmes Edward C, Zhang Yong-Zhen", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32015508", "url": "https://glygen.org/publication/PubMed/32015508" } ] }, { "title": "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, Becker S, Rox K, Hilgenfeld R", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32198291", "url": "https://glygen.org/publication/PubMed/32198291" } ] }, { "title": "Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.", "journal": "Nature", "date": "2020-06", "authors": "Jin Zhenming, Du Xiaoyu, Xu Yechun, Deng Yongqiang, Liu Meiqin, Zhao Yao, Zhang Bing, Li Xiaofeng, Zhang Leike, Peng Chao, Duan Yinkai, Yu Jing, Wang Lin, Yang Kailin, Liu Fengjiang, Jiang Rendi, Yang Xinglou, You Tian, Liu Xiaoce, Yang Xiuna, Bai Fang, Liu Hong, Liu Xiang, Guddat Luke W, Xu Wenqing, Xiao Gengfu, Qin Chengfeng, Shi Zhengli, Jiang Hualiang, Rao Zihe, Yang Haitao", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32272481", "url": "https://glygen.org/publication/PubMed/32272481" } ] }, { "title": "Structure of the RNA-dependent RNA polymerase from COVID-19 virus.", "journal": "Science (New York, N.Y.)", "date": "2020-05-15", "authors": "Gao Yan, Yan Liming, Huang Yucen, Liu Fengjiang, Zhao Yao, Cao Lin, Wang Tao, Sun Qianqian, Ming Zhenhua, Zhang Lianqi, Ge Ji, Zheng Litao, Zhang Ying, Wang Haofeng, Zhu Yan, Zhu Chen, Hu Tianyu, Hua Tian, Zhang Bing, Yang Xiuna, Li Jun, Yang Haitao, Liu Zhijie, Xu Wenqing, Guddat Luke W, Wang Quan, Lou Zhiyong, Rao Zihe", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32277040", "url": "https://glygen.org/publication/PubMed/32277040" } ] }, { "title": "Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.", "journal": "Science (New York, N.Y.)", "date": "2020-06-19", "authors": "Dai Wenhao, Zhang Bing, Jiang Xia-Ming, Su Haixia, Li Jian, Zhao Yao, Xie Xiong, Jin Zhenming, Peng Jingjing, Liu Fengjiang, Li Chunpu, Li You, Bai Fang, Wang Haofeng, Cheng Xi, Cen Xiaobo, Hu Shulei, Yang Xiuna, Wang Jiang, Liu Xiang, Xiao Gengfu, Jiang Hualiang, Rao Zihe, Zhang Lei-Ke, Xu Yechun, Yang Haitao, Liu Hong", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32321856", "url": "https://glygen.org/publication/PubMed/32321856" } ] }, { "title": "Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Yin W, Mao C, Luan X, Shen DD, Shen Q, Su H, Wang X, Zhou F, Zhao W, Gao M, Chang S, Xie YC, Tian G, Jiang HW, Tao SC, Shen J, Jiang Y, Jiang H, Xu Y, Zhang S, Zhang Y, Xu HE", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32358203", "url": "https://glygen.org/publication/PubMed/32358203" } ] }, { "title": "Structure of replicating SARS-CoV-2 polymerase.", "journal": "Nature", "date": "2020-08", "authors": "Hillen Hauke S, Kokic Goran, Farnung Lucas, Dienemann Christian, Tegunov Dimitry, Cramer Patrick", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32438371", "url": "https://glygen.org/publication/PubMed/32438371" } ] }, { "title": "Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.", "journal": "Cell", "date": "2020", "authors": "Wang Q, Wu J, Wang H, Gao Y, Liu Q, Mu A, Ji W, Yan L, Zhu Y, Zhu C, Fang X, Yang X, Huang Y, Gao H, Liu F, Ge J, Sun Q, Yang X, Xu W, Liu Z, Yang H, Lou Z, Jiang B, Guddat LW, Gong P, Rao Z", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32526208", "url": "https://glygen.org/publication/PubMed/32526208" } ] }, { "title": "Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3.", "journal": "Biochemistry", "date": "2020-07-21", "authors": "Frick David N, Virdi Rajdeep S, Vuksanovic Nemanja, Dahal Narayan, Silvaggi Nicholas R", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32578982", "url": "https://glygen.org/publication/PubMed/32578982" } ] }, { "title": "SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls.", "journal": "Nature", "date": "2020-08", "authors": "Le Bert Nina, Tan Anthony T, Kunasegaran Kamini, Tham Christine Y L, Hafezi Morteza, Chia Adeline, Chng Melissa Hui Yen, Lin Meiyin, Tan Nicole, Linster Martin, Chia Wan Ni, Chen Mark I-Cheng, Wang Lin-Fa, Ooi Eng Eong, Kalimuddin Shirin, Tambyah Paul Anantharajah, Low Jenny Guek-Hong, Tan Yee-Joo, Bertoletti Antonio", "evidence": [ { "database": "IEDB", "id": "1146707", "url": "https://www.iedb.org/epitope/1146707" }, { "database": "IEDB", "id": "1167599", "url": "https://www.iedb.org/epitope/1167599" }, { "database": "IEDB", "id": "1169536", "url": "https://www.iedb.org/epitope/1169536" } ], "reference": [ { "type": "PubMed", "id": "32668444", "url": "https://glygen.org/publication/PubMed/32668444" } ] }, { "title": "Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.", "journal": "Science (New York, N.Y.)", "date": "2020", "authors": "Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32680882", "url": "https://glygen.org/publication/PubMed/32680882" } ] }, { "title": "Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.", "journal": "Nature", "date": "2020", "authors": "Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Muller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32726803", "url": "https://glygen.org/publication/PubMed/32726803" } ] }, { "title": "Activation and evasion of type I interferon responses by SARS-CoV-2.", "journal": "Nature communications", "date": "2020-07-30", "authors": "Lei Xiaobo, Dong Xiaojing, Ma Ruiyi, Wang Wenjing, Xiao Xia, Tian Zhongqin, Wang Conghui, Wang Ying, Li Li, Ren Lili, Guo Fei, Zhao Zhendong, Zhou Zhuo, Xiang Zichun, Wang Jianwei", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32733001", "url": "https://glygen.org/publication/PubMed/32733001" } ] }, { "title": "A molecular pore spans the double membrane of the coronavirus replication organelle.", "journal": "Science", "date": "2020", "authors": "Wolff Georg, Limpens Ronald W A L, Zevenhoven-Dobbe Jessika C, Laugks Ulrike, Zheng Shawn, de Jong Anja W M, Koning Roman I, Agard David A, Gr\u00fcnewald Kay, Koster Abraham J, Snijder Eric J, B\u00e1rcena Montserrat", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "32763915", "url": "https://glygen.org/publication/PubMed/32763915" } ] }, { "title": "Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes.", "journal": "Genome medicine", "date": "2020-08-13", "authors": "Poran Asaf, Harjanto Dewi, Malloy Matthew, Arieta Christina M, Rothenberg Daniel A, Lenkala Divya, van Buuren Marit M, Addona Terri A, Rooney Michael S, Srinivasan Lakshmi, Gaynor Richard B", "evidence": [ { "database": "IEDB", "id": "16743", "url": "https://www.iedb.org/epitope/16743" }, { "database": "IEDB", "id": "1125057", "url": "https://www.iedb.org/epitope/1125057" } ], "reference": [ { "type": "PubMed", "id": "32791978", "url": "https://glygen.org/publication/PubMed/32791978" } ] }, { "title": "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.", "journal": "Nature structural & molecular biology", "date": "2020", "authors": "Schubert K, Karousis ED, Jomaa A, Scaiola A, Echeverria B, Gurzeler LA, Leibundgut M, Thiel V, Muhlemann O, Ban N", "evidence": [ { 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Adv.", "date": "2022", "authors": "Bessa Luiza Mamigonian, Guseva Serafima, Camacho-Zarco Aldo R, Salvi Nicola, Maurin Damien, Perez Laura Mari\u00f1o, Botova Maiia, Malki Anas, Nanao Max, Jensen Malene Ringkj\u00f8bing, Ruigrok Rob W H, Blackledge Martin", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35044811", "url": "https://glygen.org/publication/PubMed/35044811" } ] }, { "title": "Longitudinal immune profiling reveals dominant epitopes mediating long-term humoral immunity in COVID-19-convalescent individuals.", "journal": "The Journal of allergy and clinical immunology", "date": "2022-04", "authors": "Li Min, Liu Jiaojiao, Lu Renfei, Zhang Yuchao, Du Meng, Xing Man, Wu Zhenchuan, Kong Xiangyin, Zhu Yufei, Zhou Xianchao, Hu Landian, Zhang Chiyu, Zhou Dongming, Jin Xia", "evidence": [ { "database": "IEDB", "id": "1861786", "url": "https://www.iedb.org/epitope/1861786" } ], "reference": [ { "type": "PubMed", "id": "35074422", "url": "https://glygen.org/publication/PubMed/35074422" } ] }, { "title": "Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair.", "journal": "Open biology", "date": "2022-02", "authors": "de Castro Mateus V, Santos Keity S, Apostolico Juliana S, Fernandes Edgar R, Almeida Rafael R, Levin Gabriel, Magawa Jhosiene Y, Nunes Jo\u00e3o Paulo S, Bruni Mirian, Yamamoto Marcio M, Lima Ariane C, Silva Monize V R, Matos Larissa R B, Coria Vivian R, Castelli Erick C, Scliar Marilia O, Kuramoto Andreia, Bruno Fernanda R, Jacintho Lucas C, Nunes Kelly, Wang Jaqueline Y T, Coelho Veronica P, Neto Miguel Mitne, Maciel Rui M B, Naslavsky Michel S, Passos-Bueno Maria Rita, Boscardin Silvia B, Rosa Daniela S, Kalil Jorge, Zatz Mayana, Cunha-Neto Edecio", "evidence": [ { "database": "IEDB", "id": "7121", "url": "https://www.iedb.org/epitope/7121" }, { "database": "IEDB", "id": "16786", "url": 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"title": "SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells.", "journal": "Nature immunology", "date": "2022-05", "authors": "Minervina Anastasia A, Pogorelyy Mikhail V, Kirk Allison M, Crawford Jeremy Chase, Allen E Kaitlynn, Chou Ching-Heng, Mettelman Robert C, Allison Kim J, Lin Chun-Yang, Brice David C, Zhu Xun, Vegesana Kasi, Wu Gang, Trivedi Sanchit, Kottapalli Pratibha, Darnell Daniel, McNeely Suzanne, Olsen Scott R, Schultz-Cherry Stacey, Estepp Jeremie H, , McGargill Maureen A, Wolf Joshua, Thomas Paul G", "evidence": [ { "database": "IEDB", "id": "72048", "url": "https://www.iedb.org/epitope/72048" }, { "database": "IEDB", "id": "1311144", "url": "https://www.iedb.org/epitope/1311144" }, { "database": "IEDB", "id": "1326307", "url": "https://www.iedb.org/epitope/1326307" } ], "reference": [ { "type": "PubMed", "id": "35383307", "url": "https://glygen.org/publication/PubMed/35383307" } ] }, { "title": "Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2.", "journal": "JCI insight", "date": "2022-05-09", "authors": "Titov Aleksei, Shaykhutdinova Regina, Shcherbakova Olga V, Serdyuk Yana V, Sheetikov Savely A, Zornikova Ksenia V, Maleeva Alexandra V, Khmelevskaya Alexandra, Dianov Dmitry V, Shakirova Naina T, Malko Dmitry B, Shkurnikov Maxim, Nersisyan Stepan, Tonevitsky Alexander, Khamaganova Ekaterina, Ershov Anton V, Osipova Elena Y, Nikolaev Ruslan V, Pershin Dmitry E, Vedmedskia Viktoria A, Maschan Michael, Ginanova Victoria R, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "32976", "url": "https://www.iedb.org/epitope/32976" }, { "database": "IEDB", "id": "55413", "url": "https://www.iedb.org/epitope/55413" }, { "database": "IEDB", "id": "72048", "url": "https://www.iedb.org/epitope/72048" }, { "database": "IEDB", "id": "1311144", "url": "https://www.iedb.org/epitope/1311144" } ], "reference": [ { "type": "PubMed", "id": "35389886", "url": "https://glygen.org/publication/PubMed/35389886" } ] }, { "title": "SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals.", "journal": "Nature microbiology", "date": "2022-05", "authors": "Lang-Meli Julia, Luxenburger Hendrik, Wild Katharina, Karl Vivien, Oberhardt Valerie, Salimi Alizei Elahe, Graeser Anne, Reinscheid Matthias, Roehlen Natascha, Reeg David B, Giese Sebastian, Ciminski Kevin, G\u00f6tz Veronika, August Dietrich, Rieg Siegbert, Waller Cornelius F, Wengenmayer Tobias, Staudacher Dawid, Huzly Daniela, Bengsch Bertram, Kochs Georg, Schwemmle Martin, Emmerich Florian, Boettler Tobias, Thimme Robert, Hofmann Maike, Neumann-Haefelin Christoph", "evidence": [ { "database": "IEDB", "id": "28050", "url": "https://www.iedb.org/epitope/28050" }, { "database": "IEDB", "id": "1310482", "url": "https://www.iedb.org/epitope/1310482" } ], "reference": [ { "type": "PubMed", "id": "35484232", "url": "https://glygen.org/publication/PubMed/35484232" } ] }, { "title": "The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle.", "journal": "Nature", "date": "2022-06", "authors": "Ricciardi Simona, Guarino Andrea Maria, Giaquinto Laura, Polishchuk Elena V, Santoro Michele, Di Tullio Giuseppe, Wilson Cathal, Panariello Francesco, Soares Vinicius C, Dias Suelen S G, Santos Julia C, Souza Thiago M L, Fusco Giovanna, Viscardi Maurizio, Brandi Sergio, Bozza Patr\u00edcia T, Polishchuk Roman S, Venditti Rossella, De Matteis Maria Antonietta", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35551511", "url": "https://glygen.org/publication/PubMed/35551511" } ] }, { "title": "Human NLRP1 is a sensor of pathogenic coronavirus 3CL proteases in lung epithelial cells.", "journal": "Molecular cell", "date": "2022", "authors": "Planes R, Pinilla M, Santoni K, Hessel A, Passemar C, Lay K, Paillette P, Valadao AC, Robinson KS, Bastard P, Lam N, Fadrique R, Rossi I, Pericat D, Bagayoko S, Leon-Icaza SA, Rombouts Y, Perouzel E, Tiraby M, Zhang Q, Cicuta P, Jouanguy E, Neyrolles O, Bryant CE, Floto AR, Goujon C, Lei FZ, Martin-Blondel G, Silva S, Casanova JL, Cougoule C, Reversade B, Marcoux J, Ravet E, Meunier E", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35594856", "url": "https://glygen.org/publication/PubMed/35594856" } ] }, { "title": "Longitudinal Assessment of SARS-CoV-2-Specific T Cell Cytokine-Producing Responses for 1 Year Reveals Persistence of Multicytokine Proliferative Responses, with Greater Immunity Associated with Disease Severity.", "journal": "Journal of virology", "date": "2022-07-13", "authors": "Lin Jonah, Law Ryan, Korosec Chapin S, Zhou Christine, Koh Wan Hon, Ghaemi Mohammad Sajjad, Samaan Philip, Ooi Hsu Kiang, Matveev Vitaliy, Yue FengYun, Gingras Anne-Claude, Estacio Antonio, Buchholz Megan, Cheatley Patti Lou, Mohammadi Avid, Kaul Rupert, Pavinski Katerina, Mubareka Samira, McGeer Allison J, Leis Jerome A, Heffernan Jane M, Ostrowski Mario", "evidence": [ { "database": "IEDB", "id": "1074924", "url": "https://www.iedb.org/epitope/1074924" }, { "database": "IEDB", "id": "1310872", "url": "https://www.iedb.org/epitope/1310872" } ], "reference": [ { "type": "PubMed", "id": "35699447", "url": "https://glygen.org/publication/PubMed/35699447" } ] }, { "title": "How the Replication and Transcription Complex Functions in Jumping Transcription of SARS-CoV-2.", "journal": "Frontiers in genetics", "date": "2022", "authors": "Liang Jianguang, Shi Jinsong, Chen Shunmei, Duan Guangyou, Yang Fan, Cheng Zhi, Li Xin, Ruan Jishou, Mi Dong, Gao Shan", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35706445", "url": "https://glygen.org/publication/PubMed/35706445" } ] }, { "title": "SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2022-08-09", "authors": "Xu Zhang, Choi Jung-Hyun, Dai David L, Luo Jun, Ladak Reese Jalal, Li Qian, Wang Yimeng, Zhang Christine, Wiebe Shane, Liu Alex C H, Ran Xiaozhuo, Yang Jiaqi, Naeli Parisa, Garzia Aitor, Zhou Lele, Mahmood Niaz, Deng Qiyun, Elaish Mohamed, Lin Rongtuan, Mahal Lara K, Hobman Tom C, Pelletier Jerry, Alain Tommy, Vidal Silvia M, Duchaine Thomas, Mazhab-Jafari Mohammad T, Mao Xiaojuan, Jafarnejad Seyed Mehdi, Sonenberg Nahum", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35878012", "url": "https://glygen.org/publication/PubMed/35878012" } ] }, { "title": "Exosomal Vaccine Loading T Cell Epitope Peptides of SARS-CoV-2 Induces Robust CD8+ T Cell Response in HLA-A Transgenic Mice.", "journal": "International journal of nanomedicine", "date": "2022", "authors": "Shen An-Ran, Jin Xiao-Xiao, Tang Tao-Tao, Ding Yan, Liu Xiao-Tao, Zhong Xin, Wu Yan-Dan, Han Xue-Lian, Zhao Guang-Yu, Shen Chuan-Lai, Lv Lin-Li, Liu Bi-Cheng", "evidence": [ { "database": "IEDB", "id": "27089", "url": "https://www.iedb.org/epitope/27089" }, { "database": "IEDB", "id": "45000", "url": "https://www.iedb.org/epitope/45000" }, { "database": "IEDB", "id": "59001", "url": "https://www.iedb.org/epitope/59001" }, { "database": "IEDB", "id": "1313218", "url": "https://www.iedb.org/epitope/1313218" }, { "database": "IEDB", "id": "1330492", "url": "https://www.iedb.org/epitope/1330492" }, { "database": "IEDB", "id": "1330571", "url": "https://www.iedb.org/epitope/1330571" }, { "database": "IEDB", "id": "1332008", "url": "https://www.iedb.org/epitope/1332008" }, { "database": "IEDB", "id": "1645287", "url": "https://www.iedb.org/epitope/1645287" }, { "database": "IEDB", "id": "1688296", "url": "https://www.iedb.org/epitope/1688296" } ], "reference": [ { "type": "PubMed", "id": "35937077", "url": "https://glygen.org/publication/PubMed/35937077" } ] }, { "title": "The mechanism of RNA capping by SARS-CoV-2.", "journal": "Nature", "date": "2022", "authors": "Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawlowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "35944563", "url": "https://glygen.org/publication/PubMed/35944563" } ] }, { "title": "Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection.", "journal": "Nature communications", "date": "2022-09-23", "authors": "Khatamzas Elham, Antwerpen Markus H, Rehn Alexandra, Graf Alexander, Hellmuth Johannes Christian, Hollaus Alexandra, Mohr Anne-Wiebe, Gaitzsch Erik, Weiglein Tobias, Georgi Enrico, Scherer Clemens, Stecher Stephanie-Susanne, Gruetzner Stefanie, Blum Helmut, Krebs Stefan, Reischer Anna, Leutbecher Alexandra, Subklewe Marion, Dick Andrea, Zange Sabine, Girl Philipp, M\u00fcller Katharina, Weigert Oliver, Hopfner Karl-Peter, Stemmler Hans-Joachim, von Bergwelt-Baildon Michael, Keppler Oliver T, W\u00f6lfel Roman, Muenchhoff Maximilian, Moosmann Andreas", "evidence": [ { "database": "IEDB", "id": "2998", "url": "https://www.iedb.org/epitope/2998" }, { "database": "IEDB", "id": "7121", "url": "https://www.iedb.org/epitope/7121" }, { "database": "IEDB", "id": "7122", "url": "https://www.iedb.org/epitope/7122" } ], "reference": [ { "type": "PubMed", "id": "36151076", "url": "https://glygen.org/publication/PubMed/36151076" } ] }, { "title": "Identification and assessment of TCR-T cells targeting an epitope conserved in SARS-CoV-2 variants for the treatment of COVID-19.", "journal": "International immunopharmacology", "date": "2022-11", "authors": "Ma Yipeng, Liu Fenglan, Li Bin, Peng Kaiqi, Zhou Hong, Xu You, Qiao Dongjuan, Deng Lijuan, Tian Geng, Nielsen Morten, Wang Mingjun", "evidence": [ { "database": "IEDB", "id": "38782", "url": "https://www.iedb.org/epitope/38782" }, { "database": "IEDB", "id": "38783", "url": "https://www.iedb.org/epitope/38783" } ], "reference": [ { "type": "PubMed", "id": "36201943", "url": "https://glygen.org/publication/PubMed/36201943" } ] }, { "title": "Parallel detection of SARS-CoV-2 epitopes reveals dynamic immunodominance profiles of CD8+ T memory cells in convalescent COVID-19 donors.", "journal": "Clinical & translational immunology", "date": "2022", "authors": "van den Dijssel Jet, Hagen Ruth R, de Jongh Rivka, Steenhuis Maurice, Rispens Theo, Geerdes Dionne M, Mok Juk Yee, Kragten Angela Hm, Duurland Mari\u00ebl C, Verstegen Niels Jm, van Ham S Marieke, van Esch Wim Je, van Gisbergen Klaas Pjm, Hombrink Pleun, Ten Brinke Anja, van de Sandt Carolien E", "evidence": [ { "database": "IEDB", "id": "28050", "url": "https://www.iedb.org/epitope/28050" }, { "database": "IEDB", "id": "72048", "url": "https://www.iedb.org/epitope/72048" }, { "database": "IEDB", "id": "1310482", "url": "https://www.iedb.org/epitope/1310482" } ], "reference": [ { "type": "PubMed", "id": "36254196", "url": "https://glygen.org/publication/PubMed/36254196" } ] }, { "title": "Nsp16 shields SARS-CoV-2 from efficient MDA5 sensing and IFIT1-mediated restriction.", "journal": "EMBO reports", "date": "2022-12-06", "authors": "Russ Alina, Wittmann Sabine, Tsukamoto Yuta, Herrmann Alexandra, Deutschmann Janina, Lagisquet Justine, Ensser Armin, Kato Hiroki, Gramberg Thomas", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "36285486", "url": "https://glygen.org/publication/PubMed/36285486" } ] }, { "title": "Clonal diversity predicts persistence of SARS-CoV-2 epitope-specific T-cell response.", "journal": "Communications biology", "date": "2022-12-09", "authors": "Zornikova Ksenia V, Khmelevskaya Alexandra, Sheetikov Savely A, Kiryukhin Dmitry O, Shcherbakova Olga V, Titov Aleksei, Zvyagin Ivan V, Efimov Grigory A", "evidence": [ { "database": "IEDB", "id": "2998", "url": "https://www.iedb.org/epitope/2998" }, { "database": "IEDB", "id": "32240", "url": "https://www.iedb.org/epitope/32240" } ], "reference": [ { "type": "PubMed", "id": "36494499", "url": "https://glygen.org/publication/PubMed/36494499" } ] }, { "title": "Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19.", "journal": "Nature communications", "date": "2022-12-16", "authors": "Ogura Hideki, Gohda Jin, Lu Xiuyuan, Yamamoto Mizuki, Takesue Yoshio, Son Aoi, Doi Sadayuki, Matsushita Kazuyuki, Isobe Fumitaka, Fukuda Yoshihiro, Huang Tai-Ping, Ueno Takamasa, Mambo Naomi, Murakami Hiromoto, Kawaguchi Yasushi, Inoue Jun-Ichiro, Shirai Kunihiro, Yamasaki Sho, Hirata Jun-Ichi, Ishido Satoshi", "evidence": [ { "database": "IEDB", "id": "72048", "url": "https://www.iedb.org/epitope/72048" } ], "reference": [ { "type": "PubMed", "id": "36526616", "url": "https://glygen.org/publication/PubMed/36526616" } ] }, { "title": "Nsp1 proteins of human coronaviruses HCoV-OC43 and SARS-CoV2 inhibit stress granule formation.", "journal": "PLoS pathogens", "date": "2022-12", "authors": "Dolliver Stacia M, Kleer Mariel, Bui-Marinos Maxwell P, Ying Shan, Corcoran Jennifer A, Khaperskyy Denys A", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "36534661", "url": "https://glygen.org/publication/PubMed/36534661" } ] }, { "title": "Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development.", "journal": "Nucleic Acids Res.", "date": "2023", "authors": "Imprachim Nergis, Yosaatmadja Yuliana, Newman Joseph A", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "36546776", "url": "https://glygen.org/publication/PubMed/36546776" } ] }, { "title": "Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes.", "journal": "Cell systems", "date": "2023-01-18", "authors": "Gfeller David, Schmidt Julien, Croce Giancarlo, Guillaume Philippe, Bobisse Sara, Genolet Raphael, Queiroz Lise, Cesbron Julien, Racle Julien, Harari Alexandre", "evidence": [ { "database": "IEDB", "id": "14969", "url": "https://www.iedb.org/epitope/14969" } ], "reference": [ { "type": "PubMed", "id": "36603583", "url": "https://glygen.org/publication/PubMed/36603583" } ] }, 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Med. Virol.", "date": "2024", "authors": "Zhou Yuzheng, Feng Wei, Yang Chuwei, Wei Xiafei, Fan Lujie, Wu Yezi, Gao Xiang, Shen Xiaotong, Zhang Zheng, Zhao Juanjuan", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "39223933", "url": "https://glygen.org/publication/PubMed/39223933" } ] }, { "title": "T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects.", "journal": "Biomolecules", "date": "2024-09-26", "authors": "Macchia Iole, La Sorsa Valentina, Ciervo Alessandra, Ruspantini Irene, Negri Donatella, Borghi Martina, De Angelis Maria Laura, Luciani Francesca, Martina Antonio, Taglieri Silvia, Durastanti Valentina, Altavista Maria Concetta, Urbani Francesca, Mancini Fabiola", "evidence": [ { "database": "IEDB", "id": "72766", "url": "https://www.iedb.org/epitope/72766" }, { "database": "IEDB", "id": "120150", "url": "https://www.iedb.org/epitope/120150" }, { "database": "IEDB", "id": "120241", "url": "https://www.iedb.org/epitope/120241" }, { "database": "IEDB", "id": "1309121", "url": "https://www.iedb.org/epitope/1309121" }, { "database": "IEDB", "id": "1311990", "url": "https://www.iedb.org/epitope/1311990" }, { "database": "IEDB", "id": "1312047", "url": "https://www.iedb.org/epitope/1312047" }, { "database": "IEDB", "id": "1312055", "url": "https://www.iedb.org/epitope/1312055" }, { "database": "IEDB", "id": "1330573", "url": "https://www.iedb.org/epitope/1330573" }, { "database": "IEDB", "id": "1331972", "url": "https://www.iedb.org/epitope/1331972" }, { "database": "IEDB", "id": "1906343", "url": "https://www.iedb.org/epitope/1906343" }, { "database": "IEDB", "id": "2134238", "url": "https://www.iedb.org/epitope/2134238" }, { "database": "IEDB", "id": "2268576", "url": "https://www.iedb.org/epitope/2268576" } ], "reference": [ { "type": "PubMed", "id": "39456150", "url": "https://glygen.org/publication/PubMed/39456150" } ] }, { "title": "Staggered immunization with mRNA vaccines encoding SARS-CoV-2 polymerase or spike antigens broadens the T cell epitope repertoire.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-12-03", "authors": "Abt Evan R, Lam Alex K, Noguchi Miyako, Rashid Khalid, McLaughlin Jami, Teng Pu-Lin, Tran Wendy, Cheng Donghui, Nesterenko Pavlo A, Mao Zhiyuan, Creech Amanda L, Burton Sojo Giselle, Jeyachandran Arjit Vijey, Tam Ying K, Henley Jill E, Comai Lucio, Pardi Norbert, Arumugaswami Vaithilingaraja, Witte Owen N, Radu Caius G, Wu Ting-Ting", "evidence": [ { "database": "IEDB", "id": "55444", "url": "https://www.iedb.org/epitope/55444" }, { "database": "IEDB", "id": "65176", "url": "https://www.iedb.org/epitope/65176" }, { "database": "IEDB", "id": "2269842", "url": "https://www.iedb.org/epitope/2269842" }, { "database": "IEDB", "id": "2269852", "url": "https://www.iedb.org/epitope/2269852" } ], "reference": [ { "type": "PubMed", "id": "39589869", "url": "https://glygen.org/publication/PubMed/39589869" } ] }, { "title": "Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease.", "journal": "eLife", "date": "2025-01-07", "authors": "D'Oliviera Angel, Dai Xuhang, Mottaghinia Saba, Olson Sophie, Geissler Evan P, Etienne Lucie, Zhang Yingkai, Mugridge Jeffrey S", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "39773525", "url": "https://glygen.org/publication/PubMed/39773525" } ] }, { "title": "The SARS-CoV-2 3CL protease inhibits pyroptosis through the cleavage of gasdermin D.", "journal": "Virologica Sinica", "date": "2025-06", "authors": "Zhang Yecheng, Ji Xinlei, Huang Dan, Lu Gen, Chen Xinwen", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "40118151", "url": "https://glygen.org/publication/PubMed/40118151" } ] }, { "title": "Human coronavirus 3CL protease manipulates host protein STIM1 to facilitate immune evasion.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2025-12-02", "authors": "Lee Yoon Young, Lee Ah Reum, Seo Seongkyung, Park Uni, Kim Taehun, Lee Sang Kwon, Jeong Hyeongsun, Jeong Su Ji, Kweon Yeong Cheon, Eun Park Go, Kim Min Ji, Kim Byung-Gyu, Kwon Taejoon, Cho Nam-Hyuk, Moo Kwon Hyug, Myung Kyungjae, Lee Sang Min, Park Chan Young", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "reference": [ { "type": "PubMed", "id": "41289387", "url": "https://glygen.org/publication/PubMed/41289387" } ] } ], "pathway": [], "orthologs": [ { "uniprot_canonical_ac": "P0C6X7-1", "protein_name": "Replicase polyprotein 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RIMASLVLARKHNTCCNLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDHEFVDEFYAYLRKHFSMMILSDDAVVCYNSNYAAQGLVASIKNFKAVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKIGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKIITGLHPTQAPTHLSVDIKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRDAVGTNLPLQLGFSTGVNLVAVPTGYVDTENNTEFTRVNAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKGLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDKRATCFSTSSDTYACWNHSVGFDYVYNPFMIDVQQWGFTGNLQSNHDQHCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWSVEYPIIGDELRVNSACRKVQHMVVKSALLADKFPVLHDIGNPKAIKCVPQAEVEWKFYDAQPCSDKAYKIEELFYSYATHHDKFTDGVCLFWNCNVDRYPANAIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFTNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRQYLDAYNMMISAGFSLWIYKQFDTYNLWNTFTRLQSLENVAYNVVNKGHFDGHAGEAPVSIINNAVYTKVDGIDVEIFENKTTLPVNVAFELWAKRNIKPVPEIKILNNLGVDIAANTVIWDYKREAPAHVSTIGVCTMTDIAKKPTESACSSLTVLFDGRVEGQVDLFRNARNGVLITEGSVKGLTPSKGPAQASVNGVTLIGESVKTQFNYFKKVDGIIQQLPETYFTQSRDLEDFKPRSQMETDFLELAMDEFIQRYKLEGYAFEHIVYGDFSHGQLGGLHLMIGLAKRSQDSPLKLEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVISKVVKVTIDYAEISFMLWCKDGHVETFYPKLQASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHSWNADLYKLMGHFSWWTAFVTNVNASSSEAFLIGANYLGKPKEQIDGYTMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKENQINDMIYSLLEKGRLIIRENNRVVVSSDILVNN", "length": 7073 }, "evidence": [ { "id": "UniRef50_P0C6X7", "url": "https://www.uniprot.org/uniref/UniRef50_P0C6X7", "database": "UniRef" } ], "glygen_name": "HCoV-SARS", "common_name": "SARS-CoV" } ], "go_annotation": { "categories": [ { "name": "Molecular Function", "total": 22, "go_terms": [ { "name": "methyltransferase cap1 activity", "id": "GO:0004483", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0004483", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "RNA-directed RNA polymerase activity", "id": "GO:0003968", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0003968", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "RNA binding", "id": "GO:0003723", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0003723", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "ATP binding", "id": "GO:0005524", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005524", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "omega peptidase activity", "id": "GO:0008242", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008242", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "zinc ion binding", "id": "GO:0008270", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008270", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "ATP hydrolysis activity", "id": "GO:0016887", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0016887", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "lipid binding", "id": "GO:0008289", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0008289", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "single-stranded RNA binding", "id": "GO:0003727", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0003727", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "copper ion binding", "id": "GO:0005507", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005507", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "G-quadruplex RNA binding", "id": "GO:0002151", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0002151", "evidence": [ { "database": "UniProtKB", "id": "P0DTD1", "url": "https://www.uniprot.org/uniprotkb/P0DTD1" } ], "pmid": "" }, { "name": "cysteine-type endopeptidase activity", 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