{ "bcoid": "GLY_000422", "title": "SARS-CoV2 Protein Function (UniProtKB)", "description": "The SARS coronavirus (SARS-CoV-2 or 2019-nCov) Protein Function (UniProtKB) dataset contains biological ...", "filename": "sarscov2_protein_function_uniprotkb.csv", "filetype": "csv", "categories": { "species": "SARS coronavirus (SARS-CoV-2 or 2019-nCoV)", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P0DTD2-1...", "protein_xref..." ], [ "P0DTC6-1...", "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": "evidence" }, { "type": "string", "label": "annotation" } ], [ "P0DTD2-1", "protein_xref_uniprotkb_fun", "P0DTD2", "", "Plays a role in inhibiting the host innate immune response by targeting the mitochondrial-associated innate immune response. Acts by binding to host TOMM70, disrupting its role in the interferon activation pathway." ], [ "P0DTC6-1", "protein_xref_uniprotkb_fun", "P0DTC6", "32979938", "Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane. Retention of import factors at the ER/Golgi membrane leads to a loss of transport into the nucleus. Thereby 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)." ], [ "P0DTC6-1", "protein_xref_uniprotkb_fun", "P0DTC6", "33097660", "Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane. Retention of import factors at the ER/Golgi membrane leads to a loss of transport into the nucleus. Thereby 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)." ], [ "P0DTC7-1", "protein_xref_uniprotkb_fun", "P0DTC7", "", "Plays a role as antagonist of host tetherin (BST2), disrupting its antiviral effect. Acts by binding to BST2 thereby interfering with its glycosylation. May suppress small interfering RNA (siRNA). May bind to host ITGAL, thereby playing a role in attachment or modulation of leukocytes." ], [ "P0DTD3-1", "protein_xref_uniprotkb_fun", "P0DTD3", "", "May play a role in host-virus interaction." ], [ "P0DTC5-1", "protein_xref_uniprotkb_fun", "P0DTC5", "33229438", "Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins (By similarity). Regulates the localization of S protein at cis-Golgi, the place of virus budding (PubMed:33229438). May act by binding cytoplasmic c-terminus of S (PubMed:33229438)." ], [ "P0DTC4-1", "protein_xref_uniprotkb_fun", "P0DTC4", "32891874", "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). Regulates the localization of S protein at cis-Golgi, the place of virus budding (PubMed:33229438). May act by slowing down the cell secretory pathway (PubMed:33229438). May interfere with tight-junction stability by interacting with host MPP5. This would result in disruption of epithelial barriers, thereby amplifying inflammatory processes (PubMed:32891874)." ], [ "P0DTC4-1", "protein_xref_uniprotkb_fun", "P0DTC4", "33229438", "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). Regulates the localization of S protein at cis-Golgi, the place of virus budding (PubMed:33229438). May act by slowing down the cell secretory pathway (PubMed:33229438). May interfere with tight-junction stability by interacting with host MPP5. This would result in disruption of epithelial barriers, thereby amplifying inflammatory processes (PubMed:32891874)." ], [ "P0DTC3-1", "protein_xref_uniprotkb_fun", "P0DTC3", "33157038", "Plays a role in virus egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporin) localized at endosomes and lysosomes, that may induce deacidification of lysosomes thereby allowing safe virion egress through lysosomal trafficking (By similarity) (PubMed:33157038, PubMed:33422265). Also blocks formation of autolysosomes through binding and sequestering host TMUB1/HOPS on late endosomes. This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265)." ], [ "P0DTC3-1", "protein_xref_uniprotkb_fun", "P0DTC3", "33422265", "Plays a role in virus egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporin) localized at endosomes and lysosomes, that may induce deacidification of lysosomes thereby allowing safe virion egress through lysosomal trafficking (By similarity) (PubMed:33157038, PubMed:33422265). Also blocks formation of autolysosomes through binding and sequestering host TMUB1/HOPS on late endosomes. This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265)." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "", "Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "", "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." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "", "May down-regulate host tetherin (BST2) by lysosomal degradation, thereby counteracting its antiviral activity." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32075877", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32142651", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32155444", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32221306", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32362314", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "32817270", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "33082293", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC2-1", "protein_xref_uniprotkb_fun", "P0DTC2", "33082294", "attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "", "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." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "", "Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "", "Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "", "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." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32979938", "Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic (By similarity). Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes (By similarity). Binds to host TBK1 without affecting TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32277040", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32358203", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32438371", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32526208", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32198291", "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). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (By similarity) (PubMed:32198291, PubMed:32272481)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32272481", "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). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (By similarity) (PubMed:32198291, PubMed:32272481)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32321856", "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). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (By similarity) (PubMed:32198291, PubMed:32272481)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32578982", "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 (By similarity). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also 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 DDX58 (RIG-I) (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32726803", "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 (By similarity). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also 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 DDX58 (RIG-I) (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32733001", "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 (By similarity). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also 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 DDX58 (RIG-I) (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "33727702", "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 (By similarity). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also 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 DDX58 (RIG-I) (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32680882", "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32908316", "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32979938", "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "33080218", "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "33479166", "Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32277040", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32358203", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32438371", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "32526208", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "33080218", "Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, 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)." ], [ "P0DTC1-1", "protein_xref_uniprotkb_fun", "P0DTC1", "33080218", "May participate in viral replication by acting as a ssRNA-binding protein (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)." ], [ "P0DTG1-1", "protein_xref_uniprotkb_fun", "P0DTG1", "", "May play a role in host modulation." ], [ "P0DTG0-1", "protein_xref_uniprotkb_fun", "P0DTG0", "", "May play a role in host modulation." ], [ "P0DTF1-1", "protein_xref_uniprotkb_fun", "P0DTF1", "", "May play a role in interferon antiviral system evasion." ], [ "P0DTC9-1", "protein_xref_uniprotkb_fun", "P0DTC9", "", "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 (By similarity). May modulate transforming growth factor-beta signaling by binding host smad3 (By similarity)." ], [ "P0DTC8-1", "protein_xref_uniprotkb_fun", "P0DTC8", "31986261", "Plays a role in modulating host immune response (PubMed:31986261). Binds to IL17RA receptor, leading to IL17 pathway activation and an increased secretion of pro-inflammatory factors. Contributes to cytokine storm during COVID-19 infection." ] ] }, "readme": "Name\n - SARS-CoV2 Protein Function (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2020-04-03T11:46:41.584409\n\nModified on\n - 2020-04-10T12:25:10.311615\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 Function (UniProtKB) dataset contains biological function annotation for sarscov2 [taxid:2697049] 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-sars-cov-2.nt\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/source/uniprot-proteome-sars-cov-2.nt\n Name: sarscov2_protein_masterlist.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_masterlist.csv\n Output Subdomain\n Name: sarscov2_protein_function_uniprotkb.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_function_uniprotkb.csv\n Name: sarscov2_protein_function_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_function_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/sarscov2_protein_function_uniprotkb.csv" }