3WRY | pdb_00003wry

Crystal structure of helicase complex 2

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	EUF08559	e3wryD2	A: a+b complex topology	X: Tomato mosaic virus helicase N-terminal domain (From Topology)	H: Tomato mosaic virus helicase N-terminal domain (From Topology)	T: Tomato mosaic virus helicase N-terminal domain	F: EUF08559	ECOD (1.6)
D	UvrD_C_2_1	e3wryD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C_2_1	ECOD (1.6)
D	Viral_helicase1	e3wryD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Viral_helicase1	ECOD (1.6)
C	EUF08559	e3wryC2	A: a+b complex topology	X: Tomato mosaic virus helicase N-terminal domain (From Topology)	H: Tomato mosaic virus helicase N-terminal domain (From Topology)	T: Tomato mosaic virus helicase N-terminal domain	F: EUF08559	ECOD (1.6)
C	UvrD_C_2_1	e3wryC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C_2_1	ECOD (1.6)
C	Viral_helicase1	e3wryC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Viral_helicase1	ECOD (1.6)
B	UPF0261_C	e3wryB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Resistance protein Tm-1 second domain	F: UPF0261_C	ECOD (1.6)
B	UPF0261_N	e3wryB1	A: a/b three-layered sandwiches	X: Resistance protein Tm-1 first domain (From Topology)	H: Resistance protein Tm-1 first domain (From Topology)	T: Resistance protein Tm-1 first domain	F: UPF0261_N	ECOD (1.6)
A	UPF0261_C	e3wryA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Resistance protein Tm-1 second domain	F: UPF0261_C	ECOD (1.6)
A	UPF0261_N	e3wryA1	A: a/b three-layered sandwiches	X: Resistance protein Tm-1 first domain (From Topology)	H: Resistance protein Tm-1 first domain (From Topology)	T: Resistance protein Tm-1 first domain	F: UPF0261_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.450.420	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.450.420	Alpha Beta	2-Layer Sandwich	Beta-Lactamase		CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.12020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Uncharacterised protein family UPF0261, NN domain	CATH (4.3.0)
B	3.40.50.12030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Uncharacterised protein family UPF0261, NC domain	CATH (4.3.0)
A	3.40.50.12020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Uncharacterised protein family UPF0261, NN domain	CATH (4.3.0)
A	3.40.50.12030	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Uncharacterised protein family UPF0261, NC domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF01443	Viral superfamily 1 RNA helicase core domain (Viral_helicase1)	Viral superfamily 1 RNA helicase core domain	This entry represents the (+) RNA virus helicase core domain. The (+) RNA virus helicase core contains two RecA-like alpha/beta domains. The N-terminal ATP-binding domain contains a parallel six-stranded alpha-sheet surrounded by four helices on one ...	This entry represents the (+) RNA virus helicase core domain. The (+) RNA virus helicase core contains two RecA-like alpha/beta domains. The N-terminal ATP-binding domain contains a parallel six-stranded alpha-sheet surrounded by four helices on one side and two helices on the other. The C-terminal domain contains a parallel four-stranded beta-sheet sandwiched between two helices on each of its sides. The (+) RNA virus helicase core is likely to bind NTP in cleft between the N terminus of the ATP-binding domain and the beginning of the C-terminal domain [2,5]. Helicase activity for this domain has been demonstrated [1]. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [3].	Domain
A, B	PF06792	Uncharacterised protein family (UPF0261) N-terminal domain (UPF0261)	Uncharacterised protein family (UPF0261) N-terminal domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Replicase large subunit	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 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 RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent activity RNA methyltransferase activity transferase activity, transferring one-carbon groups methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA methyltransferase activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity RNA binding nucleic acid binding	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 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 mRNA modification mRNA metabolic process RNA modification macromolecule modification gene expression RNA processing symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction DNA-templated transcription	-
A, B	Tm-1 protein	catalytic activity 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 catalytic activity 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity	biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus RNA metabolic process viral life cycle primary metabolic process host-mediated perturbation of viral process biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus RNA metabolic process viral life cycle primary metabolic process host-mediated perturbation of viral process nucleobase-containing compound biosynthetic process host-mediated perturbation of viral RNA genome replication macromolecule biosynthetic process nucleic acid metabolic process host-mediated perturbation of symbiont 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 modulation of process of another organism	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C, D	IPR001788	RNA-dependent RNA polymerase, alsuviricetes	Domain
C, D	IPR002588	Alphavirus-like methyltransferase domain	Domain
C, D	IPR027351	(+) RNA virus helicase core domain	Domain
C, D	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C, D	IPR047310	RNA-dependent RNA polymerase, virgavirus	Domain
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR051353	Tobamovirus Resistance UPF0261	Family
A, B	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B	IPR009215	TIM-barrel domain, IGPS-like	Domain
A, B	IPR044122	UPF0261, N-terminal domain	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR056778	UPF0261, C-terminal domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.