{ "bcoid": "GLY_000421", "title": "SARS-CoV1 Protein Function (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-1) Protein Function (UniProtKB) dataset contains biological function annotation ...", "filename": "sarscov1_protein_function_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-1)", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P59596-1...", "UniProtKB..." ], [ "P0C6U8-1...", "UniProtKB..." ] ], "headers": [ "uniprotkb_ca...", "database_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_name" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "P59596-1", "UniProtKB", "P59596", "", "Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins." ], [ "P0C6U8-1", "UniProtKB", "P0C6U8", "", "Nsp9 is a ssRNA-binding protein." ], [ "P0C6U8-1", "UniProtKB", "P0C6U8", "", "The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity). Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function." ], [ "P0C6U8-1", "UniProtKB", "P0C6U8", "", "The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3." ], [ "P0C6U8-1", "UniProtKB", "P0C6U8", "", "binds to the 40S ribosomal subunit and inhibits host translation. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response." ], [ "P0C6U8-1", "UniProtKB", "P0C6U8", "", "Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter." ], [ "P59594-1", "UniProtKB", "P59594", "", "Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis." ], [ "P59594-1", "UniProtKB", "P59594", "", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 and CLEC4M/DC-SIGNR receptors and internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P59594-1", "UniProtKB", "P59594", "", "mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. 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 viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes." ], [ "P59595-1", "UniProtKB", "P59595", "", "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. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication." ], [ "Q80H93-1", "UniProtKB", "Q80H93", "", "Non-structural protein which is dispensable for virus replication in cell culture." ], [ "P59635-1", "UniProtKB", "P59635", "", "Non-structural protein which is dispensable for virus replication in cell culture." ], [ "P59633-1", "UniProtKB", "P59633", "", "Induces host cell G0/G1 arrest and apoptosis." ], [ "P59632-1", "UniProtKB", "P59632", "", "Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release. Up-regulates expression of fibrinogen subunits FGA, FGB and FGG in host lung epithelial cells. Induces apoptosis in cell culture. Downregulates the type 1 interferon receptor by inducing serine phosphorylation within the IFN alpha-receptor subunit 1 (IFNAR1) degradation motif and increasing IFNAR1 ubiquitination." ], [ "P59637-1", "UniProtKB", "P59637", "", "Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis (By similarity). Activates the host NLRP3 inflammasome, leading to IL-1beta overproduction." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "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." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Proteinase 3CL-PRO: Ccleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP)." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Responsible for replication and transcription of the viral RNA genome." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "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." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "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." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses." ], [ "P0C6X7-1", "UniProtKB", "P0C6X7", "", "May participate in viral replication by acting as a ssRNA-binding protein." ], [ "P59634-1", "UniProtKB", "P59634", "", "Could be a determinant of virus virulence, since, when expressed in an otherwise attenuated JHM strain of murine coronavirus, it can dramatically increase the lethality of the latter. Seems to stimulate cellular DNA synthesis in vitro." ] ] }, "readme": "Name\n - SARS-CoV1 Protein Function (UniProtKB)\n\nVersion\n - 1.5.23\n\nCreated on\n - 2020-04-02T23:52:06.244702\n\nModified on\n - 2020-04-09T18:41:33.892961\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@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-1) Protein Function (UniProtKB) dataset contains biological function annotation for sarscov1 [taxid:694009] protein accesions from the UniProtKB database. The dataset is derived from 2020-01 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - protein function\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB function annotations triplestore containing triples from nt file and extracts the data as a csv dataset\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-human-sars-coronavirus.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/source/uniprot-proteome-human-sars-coronavirus.nt\n Name: sarscov1_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/sarscov1_protein_masterlist.csv\n Output Subdomain\n Name: sarscov1_protein_function_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/sarscov1_protein_function_uniprotkb.csv\n Name: sarscov1_protein_function_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.23/reviewed/sarscov1_protein_function_uniprotkb.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"11\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"11\"\n Name: \"database_name\"\n Description: \"The name of the source database\"\n Unique Values: \"1\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"31\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.5.23/reviewed/sarscov1_protein_function_uniprotkb.csv" }