5YM6

Crystal Structure of porcine delta coronavirus nsp9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ym6a_	All beta proteins	Replicase NSP9	Replicase NSP9	automated matches	automated matches	(Porcine coronavirus HKU15 ) [TaxId: 1159905 ],	SCOPe (2.08)
B	d5ym6b_	All beta proteins	Replicase NSP9	Replicase NSP9	automated matches	automated matches	(Porcine coronavirus HKU15 ) [TaxId: 1159905 ],	SCOPe (2.08)
D	d5ym6d_	All beta proteins	Replicase NSP9	Replicase NSP9	automated matches	automated matches	(Porcine coronavirus HKU15 ) [TaxId: 1159905 ],	SCOPe (2.08)
C	d5ym6c_	All beta proteins	Replicase NSP9	Replicase NSP9	automated matches	automated matches	(Porcine coronavirus HKU15 ) [TaxId: 1159905 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SARS coronavirus NSP9 RNA-replicase	8076496	4000892	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SARS coronavirus NSP9 RNA-replicase	8076497	3001908	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SARS coronavirus NSP9 RNA-replicase	8076497	3001908	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SARS coronavirus NSP9 RNA-replicase	8076497	3001908	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SARS coronavirus NSP9 RNA-replicase	8076497	3001908	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	nsp9	e5ym6A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: nsp9	ECOD (1.6)
B	nsp9	e5ym6B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: nsp9	ECOD (1.6)
D	nsp9	e5ym6D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: nsp9	ECOD (1.6)
C	nsp9	e5ym6C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: nsp9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.10.250	Mainly Beta	Beta Barrel	Thrombin, subunit H	Replicase NSP9	CATH (utative)
B	2.40.10.250	Mainly Beta	Beta Barrel	Thrombin, subunit H	Replicase NSP9	CATH (utative)
D	2.40.10.250	Mainly Beta	Beta Barrel	Thrombin, subunit H	Replicase NSP9	CATH (utative)
C	2.40.10.250	Mainly Beta	Beta Barrel	Thrombin, subunit H	Replicase NSP9	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	nsp9	peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity peptidase activity omega peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity 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 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 helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity endonuclease activity identical protein binding protein binding RNA methyltransferase activity O-methyltransferase activity transferase activity, transferring one-carbon groups mRNA (nucleoside-2'-O-)-methyltransferase activity transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity mRNA methyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity lyase activity RNA binding nucleic acid binding cation binding transition metal ion binding zinc ion binding metal 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process viral genome replication biosynthetic process viral RNA genome replication organic cyclic compound biosynthetic process viral process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process viral gene expression viral protein processing gene expression DNA-templated transcription symbiont-mediated perturbation of host cellular process catabolic process regulation of cellular process biological process involved in interspecies interaction between organisms autophagy positive regulation of biological process modulation by virus of host process positive regulation of cellular metabolic process regulation of autophagy biological process involved in symbiotic interaction cellular catabolic process positive regulation of metabolic process induction by virus of host autophagy process utilizing autophagic mechanism modulation of process of another organism positive regulation of cellular process modulation by virus of host cellular process positive regulation of autophagy regulation of biological process modulation by virus of host autophagy biological regulation regulation of cellular metabolic process regulation of catabolic process symbiont-mediated perturbation of host autophagy biological process involved in interaction with host positive regulation of catabolic process modulation by symbiont of host process regulation of cellular catabolic process positive regulation of cellular catabolic process regulation of metabolic process organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular membrane-bounded organelle host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm membrane cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle endoplasmic reticulum-Golgi intermediate compartment cytoplasm intracellular membrane-bounded organelle 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 host cell cytoplasm part host intracellular organelle host cell perinuclear region of cytoplasm host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR042515	Non-structural protein NSP15, N-terminal domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR048673	Nonstructural protein 13, stalk domain, coronavirus	Domain
A, B, C, D	IPR046435	NSP14, guanine-N7-methyltransferase domain, coronavirus	Domain
A, B, C, D	IPR043174	Non-structural protein NSP15, middle domain superfamily	Homologous Superfamily
A, B, C, D	IPR044365	Non-structural protein 6, deltacoronavirus	Domain
A, B, C, D	IPR009469	RNA-dependent RNA polymerase, N-terminal, coronavirus	Domain
A, B, C, D	IPR043611	Coronavirus replicase NSP3, C-terminal	Domain
A, B, C, D	IPR038123	Non-structural protein NSP4, C-terminal superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR047566	Coronavirus replicase NSP3, Y domain	Domain
A, B, C, D	IPR044317	Nonstructural protein 14, deltacoronavirus	Domain
A, B, C, D	IPR043178	Papain-like protease, thumb domain superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR046441	RNA-dependent RNA polymerase, coronavirus	Domain
A, B, C, D	IPR048672	Nonstructural protein 13, zinc-binding domain, coronavirus	Domain
A, B, C, D	IPR043612	Non-structural protein NSP4, N-terminal, coronavirus	Domain
A, B, C, D	IPR044863	Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain	Domain
A, B, C, D	IPR044343	Nonstructural protein 13, 1B domain, coronavirus	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR043608	Nonstructural protein 15, middle domain, coronavirus	Domain
A, B, C, D	IPR037227	Endoribonuclease EndoU-like	Homologous Superfamily
A, B, C, D	IPR027352	Nonstructural protein 13, zinc-binding domain, coronavirus-like	Domain
A, B, C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D	IPR044383	Non-structural protein 2, IBV-like	Domain
A, B, C, D	IPR044354	RNA-dependent RNA polymerase, deltacoronavirus	Domain
A, B, C, D	IPR013016	Peptidase C16, coronavirus	Domain
A, B, C, D	IPR037204	Non-structural protein NSP7 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR009466	Non-structural protein 14, coronavirus	Domain
A, B, C, D	IPR046436	Nidovirus 3'-5' exoribonuclease domain	Domain
A, B, C, D	IPR047570	NSP12, interface domain, coronavirus	Domain
A, B, C, D	IPR043610	Non-structural protein 6, coronavirus	Domain
A, B, C, D	IPR027351	(+) RNA virus helicase core domain	Domain
A, B, C, D	IPR009461	Non-structural protein NSP16, coronavirus-like	Domain
A, B, C, D	IPR043477	Peptidase C30, domain 3, coronavirus	Homologous Superfamily
A, B, C, D	IPR018995	RNA synthesis protein NSP10, coronavirus	Domain
A, B, C, D	IPR044331	Nonstructural protein 15, N-terminal, deltacoronavirus	Domain
A, B, C, D	IPR045055	DNA2/NAM7-like helicase	Family
A, B, C, D	IPR043606	Coronavirus replicase NSP15, N-terminal oligomerization	Domain
A, B, C, D	IPR044307	Non-structural protein 5, deltacoronavirus	Domain
A, B, C, D	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B, C, D	IPR044401	NSP15, NendoU domain, coronavirus	Domain
A, B, C, D	IPR014822	Non-structural protein NSP9, coronavirus	Domain
A, B, C, D	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B, C, D	IPR037230	Non-structural protein NSP8 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR046440	Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain	Domain
A, B, C, D	IPR014828	Non-structural protein NSP7, coronavirus	Domain
A, B, C, D	IPR032505	Non-structural protein NSP4, C-terminal, coronavirus	Domain
A, B, C, D	IPR014829	Non-structural protein NSP8, coronavirus	Domain
A, B, C, D	IPR044324	Nonstructural protein 15, middle domain, deltacoronavirus	Domain
A, B, C, D	IPR046438	Nidovirus 2-O-methyltransferase	Domain
A, B, C, D	IPR036499	Non-structural protein NSP9 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR002589	Macro domain	Domain
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR008740	Peptidase C30, coronavirus	Domain
A, B, C, D	IPR036333	RNA synthesis protein NSP10 superfamily, coronavirus	Homologous Superfamily
A, B, C, D	IPR043472	Macro domain-like	Homologous Superfamily
A, B, C, D	IPR043609	NendoU domain, nidovirus	Domain
A, B, C, D	IPR044371	Non-structural protein 3, X-domain-like	Domain
A, B, C, D	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain