Annotations: 8SQK

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8092559	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8092559	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus NSP8-like	8092561	3000855	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SARS coronavirus NSP8-like	8092561	3000855	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus NSP7-like	8092555	3001013	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	SARS coronavirus NSP9 RNA-replicase	8092465	3001908	SCOP2B (2022-06-29)

Chains

Type

Family Name

Domain Identifier

Family Identifier

Provenance Source (Version)

SCOP2B Superfamily

Nucleotide cyclase/DNA polymerase palm domain-like

8092559

3001272

SCOP2B (2022-06-29)

SCOP2B Superfamily

Nucleotide cyclase/DNA polymerase palm domain-like

8092559

3001272

SCOP2B (2022-06-29)

SCOP2B Superfamily

SARS coronavirus NSP8-like

8092561

3000855

SCOP2B (2022-06-29)

SCOP2B Superfamily

SARS coronavirus NSP8-like

8092561

3000855

SCOP2B (2022-06-29)

SCOP2B Superfamily

SARS coronavirus NSP7-like

8092555

3001013

SCOP2B (2022-06-29)

E [auth G]

SCOP2B Superfamily

SARS coronavirus NSP9 RNA-replicase

8092465

3001908

SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00680	Viral RNA-dependent RNA polymerase (RdRP_1)	Viral RNA-dependent RNA polymerase	-	Family
A	PF06478	Coronavirus RNA-dependent RNA polymerase, N-terminal (CoV_RPol_N)	Coronavirus RNA-dependent RNA polymerase, N-terminal	This domain covers the N-terminal region of the coronavirus RNA-directed RNA Polymerase which corresponds to the nonstructural protein 12 (NSP12) produced by cleavage of ORF1b. NSP12 contains a polymerase domain that assumes a structure resembling a ...	This domain covers the N-terminal region of the coronavirus RNA-directed RNA Polymerase which corresponds to the nonstructural protein 12 (NSP12) produced by cleavage of ORF1b. NSP12 contains a polymerase domain that assumes a structure resembling a cupped 'right hand', similar to other polymerases, containing a fingers domain, a palm domain and a thumb domain. Coronavirus NSP12 also contains a nidovirus-unique N-terminal extension (nidovirus RdRp-associated nucleotidyltransferase (NiRAN) that possesses a kinase-like fold allowing the binding of NSP12 to NSP7 and NSP8. NSP12 possesses some minimal activity on its own, but the addition of the NSP7 and NSP8 co-factors greatly stimulates polymerase activity [1,2,3,4]. This domain represents the N-terminal region of the coronavirus RNA-directed RNA Polymerase, which includes the NiRAN and interface domains [1,4]. The function of the NiRAN domain is not clear and its target is yet unknown, but it has enzymatic activity that is essential for viral propagation. Structure from SARS-CoV-2 revealed that this domain binds ADP-Mg+2, which may constitute a new pocket for anti-viral treatment development [5].	Domain
E [auth G]	PF08710	Coronavirus replicase NSP9 (CoV_NSP9)	Coronavirus replicase NSP9	Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis [1]. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and high ...	Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis [1]. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerisation [2]. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication.	Domain

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA-directed RNA polymerase nsp12	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity helicase activity ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity lipid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters RNA endonuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA zinc ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus signaling biological regulation biological process involved in interaction with host canonical NF-kappaB signal transduction intracellular signal transduction biological process involved in symbiotic interaction cell communication symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host process intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus viral gene expression viral protein processing symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity gene expression DNA-templated transcription negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated suppression of host toll-like receptor signaling pathway viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell 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 endosome host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell Golgi apparatus
B, D	Non-structural protein 8	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity helicase activity ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity lipid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters RNA endonuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA zinc ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus signaling biological regulation biological process involved in interaction with host canonical NF-kappaB signal transduction intracellular signal transduction biological process involved in symbiotic interaction cell communication symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host process intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus viral gene expression viral protein processing symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity gene expression DNA-templated transcription negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated suppression of host toll-like receptor signaling pathway viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell 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 endosome host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell Golgi apparatus
C	Non-structural protein 7	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity helicase activity ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity lipid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters RNA endonuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA zinc ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus signaling biological regulation biological process involved in interaction with host canonical NF-kappaB signal transduction intracellular signal transduction biological process involved in symbiotic interaction cell communication symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host process intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus viral gene expression viral protein processing symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity gene expression DNA-templated transcription negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated suppression of host toll-like receptor signaling pathway viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell 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 endosome host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell Golgi apparatus
E [auth G]	Non-structural protein 9	protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity helicase activity ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity lipid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters endonuclease activity RNA endonuclease activity, producing 3'-phosphomonoesters RNA endonuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein cation binding transition metal ion binding copper ion binding metal ion binding O-methyltransferase activity mRNA (nucleoside-2'-O-)-methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity ISG15-specific peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding single-stranded RNA binding cysteine-type deubiquitinase activity deubiquitinase activity G-quadruplex RNA binding 5'-3' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA zinc ion binding	cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process cellular response to stimulus symbiont-mediated perturbation of host cellular process regulation of biological process biological process involved in interspecies interaction between organisms regulation of cellular process response to stimulus signaling biological regulation biological process involved in interaction with host canonical NF-kappaB signal transduction intracellular signal transduction biological process involved in symbiotic interaction cell communication symbiont-mediated perturbation of host NF-kappaB cascade symbiont-mediated perturbation of host process intracellular signaling cassette signal transduction symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host NF-kappaB cascade modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation response to host defenses response to other organism symbiont-mediated perturbation of host immune response response to defenses of other organism symbiont-mediated perturbation of host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response response to host immune response symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host innate immune response response to host response to external biotic stimulus viral gene expression viral protein processing symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway modulation by virus of host process virus-mediated perturbation of host defense response modulation by virus of host cellular process symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity gene expression DNA-templated transcription negative regulation of biological process symbiont-mediated perturbation of host translation negative regulation of cellular metabolic process symbiont-mediated suppression of host gene expression RNA catabolic process mRNA catabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process symbiont-mediated degradation of host mRNA nucleic acid catabolic process symbiont-mediated suppression of host translation regulation of macromolecule biosynthetic process symbiont-mediated perturbation of host gene expression regulation of metabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process mRNA metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process symbiont-mediated perturbation of host ubiquitin-like protein modification autophagy positive regulation of biological process positive regulation of cellular metabolic process regulation of autophagy cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism positive regulation of cellular process positive regulation of autophagy modulation by virus of host autophagy regulation of catabolic process positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated suppression of host toll-like receptor signaling pathway viral translational frameshifting viral translation proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell membrane host cell cytoplasmic vesicle membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell part host intracellular region cellular anatomical entity host cell cytoplasm part host intracellular organelle cytoplasmic viral factory double membrane vesicle viral factory membrane host cell 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 endosome host cell nucleus membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell Golgi apparatus
G [auth T]	Template RNA	-	-	-
H [auth O]	SARS-CoV-2 5' UTR	-	-	-
F [auth P]	Primer RNA	-	-	-

Chains

Polymer

Molecular Function

Biological Process

Cellular Component

RNA-directed RNA polymerase nsp12

protein guanylyltransferase activity

guanylyltransferase activity

transferase activity

nucleotidyltransferase activity

catalytic activity

transferase activity, transferring phosphorus-containing groups

3'-5'-RNA exonuclease activity

catalytic activity, acting on RNA

RNA exonuclease activity, producing 5'-phosphomonoesters

catalytic activity, acting on a nucleic acid

3'-5' exonuclease activity

RNA exonuclease activity

RNA nuclease activity

hydrolase activity

cellular biosynthetic process

cellular metabolic process

RNA metabolic process

viral life cycle

primary metabolic process

nucleobase-containing compound biosynthetic process

macromolecule biosynthetic process

nucleic acid metabolic process

RNA biosynthetic process

nucleobase-containing compound metabolic process

nucleic acid biosynthetic process

viral genome replication

biosynthetic process

viral RNA genome replication

viral process

host intracellular membrane-bounded organelle

host cellular component

host intracellular part

host cell endoplasmic reticulum-Golgi intermediate compartment

host cell cytoplasm

host cell part

host intracellular region

cellular anatomical entity

host cell cytoplasm part

host intracellular organelle

cytoplasmic viral factory

double membrane vesicle viral factory membrane

host cell membrane

host cell cytoplasmic vesicle membrane

B, D

Non-structural protein 8

protein guanylyltransferase activity

guanylyltransferase activity

transferase activity

nucleotidyltransferase activity

catalytic activity

transferase activity, transferring phosphorus-containing groups

3'-5'-RNA exonuclease activity

catalytic activity, acting on RNA

RNA exonuclease activity, producing 5'-phosphomonoesters

catalytic activity, acting on a nucleic acid

3'-5' exonuclease activity

RNA exonuclease activity

RNA nuclease activity

hydrolase activity

cellular biosynthetic process

cellular metabolic process

RNA metabolic process

viral life cycle

primary metabolic process

nucleobase-containing compound biosynthetic process

macromolecule biosynthetic process

nucleic acid metabolic process

RNA biosynthetic process

nucleobase-containing compound metabolic process

nucleic acid biosynthetic process

viral genome replication

biosynthetic process

viral RNA genome replication

viral process

host intracellular membrane-bounded organelle

host cellular component

host intracellular part

host cell endoplasmic reticulum-Golgi intermediate compartment

host cell cytoplasm

host cell part

host intracellular region

cellular anatomical entity

host cell cytoplasm part

host intracellular organelle

cytoplasmic viral factory

double membrane vesicle viral factory membrane

host cell membrane

host cell cytoplasmic vesicle membrane

Non-structural protein 7

protein guanylyltransferase activity

guanylyltransferase activity

transferase activity

nucleotidyltransferase activity

catalytic activity

transferase activity, transferring phosphorus-containing groups

3'-5'-RNA exonuclease activity

catalytic activity, acting on RNA

RNA exonuclease activity, producing 5'-phosphomonoesters

catalytic activity, acting on a nucleic acid

3'-5' exonuclease activity

RNA exonuclease activity

RNA nuclease activity

hydrolase activity

cellular biosynthetic process

cellular metabolic process

RNA metabolic process

viral life cycle

primary metabolic process

nucleobase-containing compound biosynthetic process

macromolecule biosynthetic process

nucleic acid metabolic process

RNA biosynthetic process

nucleobase-containing compound metabolic process

nucleic acid biosynthetic process

viral genome replication

biosynthetic process

viral RNA genome replication

viral process

host intracellular membrane-bounded organelle

host cellular component

host intracellular part

host cell endoplasmic reticulum-Golgi intermediate compartment

host cell cytoplasm

host cell part

host intracellular region

cellular anatomical entity

host cell cytoplasm part

host intracellular organelle

cytoplasmic viral factory

double membrane vesicle viral factory membrane

host cell membrane

host cell cytoplasmic vesicle membrane

E [auth G]

Non-structural protein 9

protein guanylyltransferase activity

guanylyltransferase activity

transferase activity

nucleotidyltransferase activity

catalytic activity

transferase activity, transferring phosphorus-containing groups

3'-5'-RNA exonuclease activity

catalytic activity, acting on RNA

RNA exonuclease activity, producing 5'-phosphomonoesters

catalytic activity, acting on a nucleic acid

3'-5' exonuclease activity

RNA exonuclease activity

RNA nuclease activity

hydrolase activity

cellular biosynthetic process

cellular metabolic process

RNA metabolic process

viral life cycle

primary metabolic process

nucleobase-containing compound biosynthetic process

macromolecule biosynthetic process

nucleic acid metabolic process

RNA biosynthetic process

nucleobase-containing compound metabolic process

nucleic acid biosynthetic process

viral genome replication

biosynthetic process

viral RNA genome replication

viral process

host intracellular membrane-bounded organelle

host cellular component

host intracellular part

host cell endoplasmic reticulum-Golgi intermediate compartment

host cell cytoplasm

host cell part

host intracellular region

cellular anatomical entity

host cell cytoplasm part

host intracellular organelle

cytoplasmic viral factory

double membrane vesicle viral factory membrane

host cell membrane

host cell cytoplasmic vesicle membrane

G [auth T]

Template RNA

H [auth O]

SARS-CoV-2 5' UTR

F [auth P]

Primer RNA

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
A	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
A	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
A	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
A	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
A	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
A	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
A	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
A	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR013016	Peptidase C16, coronavirus	Domain
A	IPR009466	Non-structural protein 14, coronavirus	Domain
A	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
A	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
A	IPR047570	NSP12, interface domain, coronavirus	Domain
A	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
A	IPR050534	Coronaviruses polyprotein 1ab	Family
A	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
A	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
A	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
A	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
A	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR008740	Peptidase C30, coronavirus	Domain
A	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
A	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
A	IPR043472	Macro domain-like	Homologous Superfamily
A	IPR043609	NendoU domain, nidovirus	Domain
A	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
A	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
A	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A	IPR044351	RNA-dependent RNA polymerase, SARS-CoV-like	Domain
A	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
A	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
A	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
A	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
A	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
A	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
A	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
A	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
A	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
A	IPR043610	Non-structural protein 6, coronavirus	Domain
A	IPR027351	(+) RNA virus helicase core domain	Domain
A	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
A	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
A	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
A	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A	IPR044401	NSP15, NendoU domain, coronavirus	Domain
A	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
A	IPR021590	NSP1, globular domain, betacoronavirus	Domain
A	IPR044367	Non-structural protein 6, betacoronavirus	Domain
A	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
A	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A	IPR046438	Nidovirus 2-O-methyltransferase	Domain
A	IPR002589	Macro domain	Domain
A	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
A	IPR044371	Non-structural protein 3, X-domain-like	Domain
A	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
B, D	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
B, D	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
B, D	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
B, D	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
B, D	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
B, D	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
B, D	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
B, D	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
B, D	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
B, D	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
B, D	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
B, D	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
B, D	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
B, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B, D	IPR013016	Peptidase C16, coronavirus	Domain
B, D	IPR009466	Non-structural protein 14, coronavirus	Domain
B, D	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
B, D	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
B, D	IPR047570	NSP12, interface domain, coronavirus	Domain
B, D	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
B, D	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
B, D	IPR050534	Coronaviruses polyprotein 1ab	Family
B, D	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
B, D	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
B, D	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
B, D	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
B, D	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
B, D	IPR014828	Non-structural protein NSP7, coronavirus	Domain
B, D	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
B, D	IPR014829	Non-structural protein NSP8, coronavirus	Domain
B, D	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
B, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, D	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
B, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B, D	IPR008740	Peptidase C30, coronavirus	Domain
B, D	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
B, D	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
B, D	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
B, D	IPR043472	Macro domain-like	Homologous Superfamily
B, D	IPR043609	NendoU domain, nidovirus	Domain
B, D	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
B, D	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
B, D	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
B, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B, D	IPR044351	RNA-dependent RNA polymerase, SARS-CoV-like	Domain
B, D	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
B, D	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
B, D	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
B, D	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
B, D	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
B, D	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
B, D	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
B, D	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
B, D	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
B, D	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
B, D	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
B, D	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
B, D	IPR043610	Non-structural protein 6, coronavirus	Domain
B, D	IPR027351	(+) RNA virus helicase core domain	Domain
B, D	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
B, D	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
B, D	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
B, D	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
B, D	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
B, D	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
B, D	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
B, D	IPR044401	NSP15, NendoU domain, coronavirus	Domain
B, D	IPR014822	Non-structural protein NSP9, coronavirus	Domain
B, D	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
B, D	IPR021590	NSP1, globular domain, betacoronavirus	Domain
B, D	IPR044367	Non-structural protein 6, betacoronavirus	Domain
B, D	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
B, D	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
B, D	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
B, D	IPR046438	Nidovirus 2-O-methyltransferase	Domain
B, D	IPR002589	Macro domain	Domain
B, D	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
B, D	IPR044371	Non-structural protein 3, X-domain-like	Domain
B, D	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
C	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
C	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
C	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
C	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
C	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
C	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
C	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
C	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
C	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
C	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
C	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
C	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C	IPR013016	Peptidase C16, coronavirus	Domain
C	IPR009466	Non-structural protein 14, coronavirus	Domain
C	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
C	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
C	IPR047570	NSP12, interface domain, coronavirus	Domain
C	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
C	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
C	IPR050534	Coronaviruses polyprotein 1ab	Family
C	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
C	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
C	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
C	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
C	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
C	IPR014828	Non-structural protein NSP7, coronavirus	Domain
C	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
C	IPR014829	Non-structural protein NSP8, coronavirus	Domain
C	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C	IPR008740	Peptidase C30, coronavirus	Domain
C	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
C	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
C	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
C	IPR043472	Macro domain-like	Homologous Superfamily
C	IPR043609	NendoU domain, nidovirus	Domain
C	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
C	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
C	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C	IPR044351	RNA-dependent RNA polymerase, SARS-CoV-like	Domain
C	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
C	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
C	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
C	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
C	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
C	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
C	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
C	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
C	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
C	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
C	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
C	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
C	IPR043610	Non-structural protein 6, coronavirus	Domain
C	IPR027351	(+) RNA virus helicase core domain	Domain
C	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
C	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
C	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
C	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
C	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
C	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
C	IPR044401	NSP15, NendoU domain, coronavirus	Domain
C	IPR014822	Non-structural protein NSP9, coronavirus	Domain
C	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
C	IPR021590	NSP1, globular domain, betacoronavirus	Domain
C	IPR044367	Non-structural protein 6, betacoronavirus	Domain
C	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
C	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
C	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
C	IPR046438	Nidovirus 2-O-methyltransferase	Domain
C	IPR002589	Macro domain	Domain
C	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
C	IPR044371	Non-structural protein 3, X-domain-like	Domain
C	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
E [auth G]	IPR022733	DPUP/SUD, C-terminal, betacoronavirus	Domain
E [auth G]	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
E [auth G]	IPR044315	Nonstructural protein 14, betacoronavirus	Domain
E [auth G]	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR042570	Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus	Homologous Superfamily
E [auth G]	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
E [auth G]	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
E [auth G]	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
E [auth G]	IPR038166	Polyprotein cleavage domain PL2pro superfamily, betacoronavirus	Homologous Superfamily
E [auth G]	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
E [auth G]	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
E [auth G]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
E [auth G]	IPR013016	Peptidase C16, coronavirus	Domain
E [auth G]	IPR009466	Non-structural protein 14, coronavirus	Domain
E [auth G]	IPR044357	NSP3, first ubiquitin-like (Ubl) domain, coronavirus	Domain
E [auth G]	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
E [auth G]	IPR047570	NSP12, interface domain, coronavirus	Domain
E [auth G]	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
E [auth G]	IPR043615	Nonstructural protein 2, N-terminal domain, coronavirus	Domain
E [auth G]	IPR050534	Coronaviruses polyprotein 1ab	Family
E [auth G]	IPR043177	Papain-like protease, N-terminal domain superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
E [auth G]	IPR044330	Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus	Domain
E [auth G]	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
E [auth G]	IPR024375	Non-structural protein NSP3, SUD-M domain, betacoronavirus	Domain
E [auth G]	IPR014828	Non-structural protein NSP7, coronavirus	Domain
E [auth G]	IPR043503	Papain-like viral protease, palm and finger domains, coronavirus	Homologous Superfamily
E [auth G]	IPR014829	Non-structural protein NSP8, coronavirus	Domain
E [auth G]	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
E [auth G]	IPR044389	Non-structural protein 2, SARS-CoV-like	Domain
E [auth G]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth G]	IPR008740	Peptidase C30, coronavirus	Domain
E [auth G]	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR047573	Non-structural protein 2, middle domain, coronavirus	Domain
E [auth G]	IPR049894	Coronavirus NSP3, 3Ecto domain	Domain
E [auth G]	IPR043472	Macro domain-like	Homologous Superfamily
E [auth G]	IPR043609	NendoU domain, nidovirus	Domain
E [auth G]	IPR032592	Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus	Domain
E [auth G]	IPR043613	Non-structural protein 2, C-terminal domain, coronavirus	Domain
E [auth G]	IPR038083	Non-structural protein NSP3A domain-like superfamily	Homologous Superfamily
E [auth G]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
E [auth G]	IPR044351	RNA-dependent RNA polymerase, SARS-CoV-like	Domain
E [auth G]	IPR024358	Non-structural protein NSP3, N-terminal, betacoronavirus	Domain
E [auth G]	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
E [auth G]	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
E [auth G]	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
E [auth G]	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
E [auth G]	IPR044864	Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus	Domain
E [auth G]	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
E [auth G]	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
E [auth G]	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
E [auth G]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth G]	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
E [auth G]	IPR044353	NSP3, second ubiquitin-like (Ubl) domain, coronavirus	Domain
E [auth G]	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR046443	NSP1, globular domain, alpha/betacoronavirus	Domain
E [auth G]	IPR043610	Non-structural protein 6, coronavirus	Domain
E [auth G]	IPR027351	(+) RNA virus helicase core domain	Domain
E [auth G]	IPR044322	Nonstructural protein 15, middle domain, alpha/betacoronavirus	Domain
E [auth G]	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
E [auth G]	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
E [auth G]	IPR043478	Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus	Homologous Superfamily
E [auth G]	IPR038400	Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus	Homologous Superfamily
E [auth G]	IPR046442	NSP1, C-terminal domain, betacoronavirus	Domain
E [auth G]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
E [auth G]	IPR044401	NSP15, NendoU domain, coronavirus	Domain
E [auth G]	IPR014822	Non-structural protein NSP9, coronavirus	Domain
E [auth G]	IPR038030	NSP1 globular domain superfamily, betacoronavirus	Homologous Superfamily
E [auth G]	IPR021590	NSP1, globular domain, betacoronavirus	Domain
E [auth G]	IPR044367	Non-structural protein 6, betacoronavirus	Domain
E [auth G]	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
E [auth G]	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
E [auth G]	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
E [auth G]	IPR046438	Nidovirus 2-O-methyltransferase	Domain
E [auth G]	IPR002589	Macro domain	Domain
E [auth G]	IPR047567	Non-structural protein NSP3, group 2-specific marker domain, betacoronavirus	Domain
E [auth G]	IPR044371	Non-structural protein 3, X-domain-like	Domain
E [auth G]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain

8SQK

SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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8SQK

SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage