3KQU | pdb_00003kqu

Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet Translocation Mechanism

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
F	d3kquf2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
F	d3kquf1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
F	d3kquf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
E	d3kque2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
E	d3kque1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
E	d3kque3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
D	d3kqud2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
D	d3kqud1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
D	d3kqud3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
C	d3kquc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
C	d3kquc1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
C	d3kquc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
B	d3kqub2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
B	d3kqub1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
B	d3kqub3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
A	d3kqua2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, C-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
A	d3kqua1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RNA helicase	HCV helicase domain, N-terminal domain	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)
A	d3kqua3	Artifacts	Tags	Tags	Tags	C-terminal Tags	HCV (Hepatitis C virus (isolate Con1) ) [TaxId: 333284 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	EUF07999	e3kquF5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
F	Helicase_C_7	e3kquF4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
F	DEAD_3	e3kquF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)
E	EUF07999	e3kquE5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
E	Helicase_C_7	e3kquE4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
E	DEAD_3	e3kquE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)
D	EUF07999	e3kquD5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
D	Helicase_C_7	e3kquD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
D	DEAD_3	e3kquD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)
C	EUF07999	e3kquC5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
C	Helicase_C_7	e3kquC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
C	DEAD_3	e3kquC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)
B	EUF07999	e3kquB5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
B	Helicase_C_7	e3kquB4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
B	DEAD_3	e3kquB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)
A	EUF07999	e3kquA5	A: alpha arrays	X: C-terminal helical domain of RNA helicase (From Topology)	H: C-terminal helical domain of RNA helicase (From Topology)	T: C-terminal helical domain of RNA helicase	F: EUF07999	ECOD (1.6)
A	Helicase_C_7	e3kquA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_7	ECOD (1.6)
A	DEAD_3	e3kquA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	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)
D	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	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)
C	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.820.10	Mainly Alpha	Orthogonal Bundle	RNA Helicase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF22027	NS3 RNA helicase, C-terminal helical domain (NS3_helicase_C)	NS3 RNA helicase, C-terminal helical domain	This entry represents the C-terminal all-alpha helical domain (referred to as domain 3) of hepatitis C virus RNA helicase (NS3) [1-5]. NS3 helicase consists of three domains, separated by a series of clefts. Bound ssDNA lies in a channel that separat ...	This entry represents the C-terminal all-alpha helical domain (referred to as domain 3) of hepatitis C virus RNA helicase (NS3) [1-5]. NS3 helicase consists of three domains, separated by a series of clefts. Bound ssDNA lies in a channel that separates domain 3 from domains 1 and 2. The 5' end of the oligonucleotide resides at the interface of domains 2 and 3 and its 3' end is positioned at the interface of domains 1. This domain is associated with domain 2 by a pair of antiparallel beta-strands [1-5].	Domain
A, B, C, D, E A, B, C, D, E, F	PF07652	Flavivirus DEAD domain (Flavi_DEAD)	Flavivirus DEAD domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth M], H [auth N]	5'-D(TTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3'	-	-	-
A, B, C, D, E A, B, C, D, E, F	Serine protease/NTPase/helicase NS3	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 peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity 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 peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity endopeptidase activity SH3 domain binding protein binding binding protein domain specific 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 nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity identical protein binding cysteine-type peptidase activity cysteine-type endopeptidase activity RNA binding nucleic acid 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 passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion 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 symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host JAK-STAT cascade biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT activity symbiont-mediated perturbation of host process symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated suppression of host TRAF-mediated signal transduction symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway symbiont-mediated transformation of host cell 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 transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport positive stranded viral RNA replication symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host proteolysis protein metabolic process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part membrane host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part membrane host intracellular membrane-bounded organelle host cell membrane host cell mitochondrion host intracellular organelle host cell mitochondrial envelope host cell mitochondrial membrane host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane viral nucleocapsid viral capsid virion component host cell plasma membrane host cell perinuclear region of cytoplasm protein-containing complex virion membrane host cell nucleus viral membrane viral envelope ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002522	Hepatitis C virus, Core protein, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR054175	NS3 RNA helicase, C-terminal helical domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011492	Non-structural protein NS3-like, DEAD-box helicase, flavivirus	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038568	Hepatitis C virus NS5A, 1B domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002868	Hepatitis C virus, Non-structural 5a protein	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038170	NS5A domain 1a superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002518	Hepatitis C virus, Non-structural protein NS2	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013192	Hepatitis C virus, Non-structural 5a protein, domain 1a	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002521	Hepatitis C virus, Core protein, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR042209	Hepatitis C virus non-structural protein NS2, N-terminal domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000745	Hepatitis C virus, Non-structural protein NS4a	Domain
A, B, C, D, E A, B, C, D, E, F	IPR042205	Hepatitis C virus non-structural protein NS2, C-terminal domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002166	RNA dependent RNA polymerase, hepatitis C virus	Family
A, B, C, D, E A, B, C, D, E, F	IPR002519	Hepatitis C virus, Envelope glycoprotein E1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR044896	Hepatitis C virus core protein, chain A superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR024350	Hepatitus C virus, Non-structural 5a protein, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013193	Hepatitis C virus non-structural 5a, 1B domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004109	Hepatitis C virus, NS3 protease	Domain
A, B, C, D, E A, B, C, D, E, F	IPR049913	Hepatitis C virus, p7 channel	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002531	Hepatitis C virus, Non-structural protein E2/NS1	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001490	Hepatitis C virus, Non-structural protein NS4b	Domain