9P0F | pdb_00009p0f

Crystal Structure of the C-terminal Cytoplasmic Domain of nsp4 from SARS-CoV-2

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF16348	Coronavirus replicase NSP4, C-terminal (CoV_NSP4_C)	Coronavirus replicase NSP4, C-terminal	This is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replicati ...	This is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex (RTC) to modified endoplasmic reticulum membranes. This predominantly alpha-helical domain may be involved in protein-protein interactions [1]. It has been shown that in Betacoronavirus, the coexpression of NSP3 and NSP4 results in a membrane rearrangement to induce double-membrane vesicles (DMVs) and convoluted membranes (CMs), playing a critical role in SARS-CoV replication. There are two well conserved amino acid residues (H120 and F121) in NSP4 among Betacoronavirus, essential for membrane rearrangements during interaction with NSP3 [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Non-structural protein 4	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity RNA binding binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding lipid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway methylation metabolic process cellular process symbiont-mediated suppression of host ISG15-protein conjugation viral gene expression viral protein processing viral process symbiont-mediated degradation of host mRNA symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway viral genome replication viral life cycle viral translational frameshifting viral translation regulation of biological process catabolic process regulation of cellular process autophagy biological regulation regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism regulation of metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane cytoplasmic viral factory double membrane vesicle viral factory membrane host cell cytoplasmic vesicle membrane host cell cytoplasmic vesicle viral factory double membrane vesicle viral factory outer membrane double membrane vesicle viral factory host cell perinuclear region of cytoplasm host cell Golgi apparatus host cell endosome host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A, B, C	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
A, B, C	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B, C	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
A, B, C	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B, C	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B, C	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C	IPR013016	Peptidase C16, coronavirus	Domain
A, B, C	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A, B, C	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A, B, C	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B, C	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B, C	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B, C	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A, B, C	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A, B, C	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
A, B, C	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A, B, C	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A, B, C	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A, B, C	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B, C	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B, C	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A, B, C	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B, C	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR002589	Macro domain	Domain
A, B, C	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A, B, C	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
A, B, C	IPR008740	Peptidase C30, coronavirus	Domain
A, B, C	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B, C	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A, B, C	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A, B, C	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A, B, C	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A, B, C	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A, B, C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily