{ "bcoid": "GLY_000472", "title": "SARS-CoV2 Protein PTM Annotation (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein PTM Annotation (UniProtKB) dataset contains sarscov2 ...", "filename": "sarscov2_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "PTM annotation", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTC7-1...", "protein_xref..." ], [ "P0DTC7-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "P0DTC7-1", "protein_xref_uniprotkb", "P0DTC7", "ECO_0000269", "Poly-ubiquitinated by host with K63-linked polyubiquitin chains." ], [ "P0DTC7-1", "protein_xref_pubmed", "33473190", "ECO_0000269", "Poly-ubiquitinated by host with K63-linked polyubiquitin chains." ], [ "P0DTC3-1", "protein_xref_uniprotkb", "P0DTC3", "ECO_0000250", "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion." ], [ "P0DTC3-1", "protein_xref_pubmed", "P59632", "ECO_0000250", "Exists in both O-glycosylated and non-glycosylated forms. The glycosylated form is associated with the virion." ], [ "P0DTC2-1", "protein_xref_uniprotkb", "P0DTC2", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32929138", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32075877", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32366695", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32363391", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32155444", "ECO_0000269", "Highly decorated by heterogeneous N-linked glycans protruding from the trimer surface (PubMed:32075877, PubMed:32155444, PubMed:32929138). Highly glycosylated by host both on S1 and S2 subunits, occluding many regions across the surface of the protein (PubMed:32366695, PubMed:32363391, 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)." ], [ "P0DTC2-1", "protein_xref_uniprotkb", "P0DTC2", "ECO_0000255", "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes." ], [ "P0DTC2-1", "protein_xref_pubmed", "MF_04099", "ECO_0000255", "The cytoplasmic Cys-rich domain is palmitoylated. Spike glycoprotein is digested within host endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb", "P0DTC2", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "33465165", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32362314", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32221306", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "32155444", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_uniprotkb", "P0DTC2", "ECO_0000255", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "MF_04099", "ECO_0000255", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC2-1", "protein_xref_pubmed", "33417835", "ECO_0000269", "Specific enzymatic cleavages in vivo yield mature proteins. The precursor is processed into S1 and S2 by host CTSL, TMPRSS2 or furin to yield the mature S1 and S2 proteins (PubMed:32155444). CTSL cleavage would occur in endosomes (PubMed:32221306, PubMed:33465165). TMPRSS2 cleavage would occur at the cell surface, allowing the virus to enter the cell despite inhibition of the endosomal pathway by hydroxychloroquine (PubMed:33465165). In addition, a second cleavage results in the release of a fusion peptide upon viral binding to the host cell receptor (By similarity). 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb", "P0DTC1", "ECO_0000250", "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed." ], [ "P0DTC1-1", "protein_xref_pubmed", "P0C6X7", "ECO_0000250", "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed." ], [ "P0DTC9-1", "protein_xref_uniprotkb", "P0DTC9", "ECO_0000255", "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection." ], [ "P0DTC9-1", "protein_xref_pubmed", "MF_04096", "ECO_0000255", "ADP-ribosylated. The ADP-ribosylation is retained in the virion during infection." ], [ "P0DTC9-1", "protein_xref_uniprotkb", "P0DTC9", "ECO_0000255", "Phosphorylated on serine and threonine residues." ], [ "P0DTC9-1", "protein_xref_pubmed", "MF_04096", "ECO_0000255", "Phosphorylated on serine and threonine residues." ], [ "P0DTD1-1", "protein_xref_uniprotkb", "P0DTD1", "ECO_0000250", "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed." ], [ "P0DTD1-1", "protein_xref_pubmed", "P0C6X7", "ECO_0000250", "Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed." ] ] }, "readme": "Name\n - SARS-CoV2 Protein PTM Annotation (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-19T11:44:49.318101\n\nModified on\n - 2022-01-13T16:44:23.378510\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The SARS coronavirus (SARS-CoV-2 or 2019-nCoV) Protein PTM Annotation (UniProtKB) dataset contains sarscov2 [taxid:2697049] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. The dataset is derived form 2020-01 UniprotKB release. If you use this dataset please give proper attribution to UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the PTM annotation strings from the triplestore for the UniProtKB canonical sequences and extracts as a dataset in a csv format. \n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-sars-cov-2.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2021_04/uniprot-proteome-sars-cov-2.nt\n Output Subdomain\n Name: sarscov2_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.csv\n Name: sarscov2_protein_ptm_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-1.12.3/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"20\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"3\"\n Name: \"ptm_annotation\"\n Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n Unique Values: \"8\"", "downloadurl": "/ln2data/releases/data/v-1.12.3/reviewed/sarscov2_protein_ptm_annotation_uniprotkb.csv" }