1S4F

Crystal Structure of RNA-dependent RNA polymerase construct 2 from bovine viral diarrhea virus (BVDV)

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	d1s4fa_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Bovine viral diarrhea virus 1 ) [TaxId: 11099 ],	SCOPe (2.08)
B	d1s4fb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Bovine viral diarrhea virus 1 ) [TaxId: 11099 ],	SCOPe (2.08)
C	d1s4fc_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Bovine viral diarrhea virus 1 ) [TaxId: 11099 ],	SCOPe (2.08)
D	d1s4fd_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Bovine viral diarrhea virus 1 ) [TaxId: 11099 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8041330	3001272	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	F_UNCLASSIFIED	e1s4fA1	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00998	e1s4fA2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00998	ECOD (1.6)
B	F_UNCLASSIFIED	e1s4fB1	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00998	e1s4fB2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00998	ECOD (1.6)
C	F_UNCLASSIFIED	e1s4fC1	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF00998	e1s4fC2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00998	ECOD (1.6)
D	F_UNCLASSIFIED	e1s4fD1	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF00998	e1s4fD2	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: PF00998	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
C	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
D	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00998	Viral RNA dependent RNA polymerase (RdRP_3)	Viral RNA dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RNA-dependent RNA polymerase	serine-type exopeptidase activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity DNA binding DNA/DNA annealing activity binding annealing activity organic cyclic compound binding single-stranded DNA binding serine-type exopeptidase activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity exopeptidase activity catalytic activity DNA binding DNA/DNA annealing activity binding annealing activity organic cyclic compound binding single-stranded DNA binding nucleic acid binding passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity serine-type endopeptidase activity endopeptidase activity RNA strand annealing activity RNA binding single-stranded RNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding endonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity phosphorus-oxygen lyase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity lyase activity ribonuclease T2 activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA ATP-dependent activity identical protein binding protein binding 5'-3' RNA polymerase activity RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cysteine-type peptidase activity cysteine-type endopeptidase activity guanyl nucleotide binding GTP binding guanyl ribonucleotide 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	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular biosynthetic process cellular metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis 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 macromolecule metabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process nucleobase-containing compound catabolic process regulation of gene expression nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of RNA metabolic process catabolic process macromolecule catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of biosynthetic process biological regulation negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression organic cyclic compound catabolic process regulation of cellular biosynthetic process RNA stabilization regulation of RNA stability organic substance catabolic process viral gene expression viral protein processing symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway response to biotic stimulus biological process involved in symbiotic interaction 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 symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response 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 biological process involved in interaction with host symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity symbiont-mediated suppression of host signal transduction pathway modulation by symbiont of host process symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway autophagy positive regulation of biological process modulation by virus of host 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 modulation by virus of host cellular process positive regulation of autophagy modulation by virus of host autophagy symbiont-mediated perturbation of host autophagy positive regulation of catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process virion assembly viral genome packaging fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transport of virus virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane 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 membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane 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 virion component virion membrane protein-containing complex protein-DNA complex ribonucleoprotein complex host cell cytoplasmic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR008751	Peptidase C53, pestivirus Npro	Domain
A, B, C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR032843	Cleavage inducing molecular chaperone, Jiv	Domain
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR021824	Capsid protein C, pestivirus	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR022120	Pestivirus nonstructural protein 2	Family
A, B, C, D	IPR049486	Flavivridae NS3 helicase, C-terminal helical domain	Domain
A, B, C, D	IPR033130	Ribonuclease T2, His active site 2	Active Site
A, B, C, D	IPR042542	Peptidase C53, pestivirus Npro, interaction domain	Homologous Superfamily
A, B, C, D	IPR030399	Pestivirus NS2, peptidase C74	Domain
A, B, C, D	IPR000280	Pestivirus NS3, peptidase S31	Domain
A, B, C, D	IPR042309	Pestivirus envelope glycoprotein E2, domain A	Homologous Superfamily
A, B, C, D	IPR042310	Pestivirus envelope glycoprotein E2, domain B	Homologous Superfamily
A, B, C, D	IPR011492	Non-structural protein NS3-like, DEAD box helicase, flavivirus	Domain
A, B, C, D	IPR002166	RNA dependent RNA polymerase, hepatitis C virus	Family
A, B, C, D	IPR042311	Pestivirus envelope glycoprotein E2, domain D	Homologous Superfamily
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR032521	Pestivirus envelope glycoprotein E2	Domain
A, B, C, D	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D	IPR036430	Ribonuclease T2-like superfamily	Homologous Superfamily