7PBT

RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s1 [t1 dataset]

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	PF05491	e7pbtA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
A	PF17864	e7pbtA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
A	PF05496	e7pbtA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
B	PF05491	e7pbtB3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
B	PF17864	e7pbtB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
B	PF05496	e7pbtB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
C	PF05491	e7pbtC3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
C	PF17864	e7pbtC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
C	PF05496	e7pbtC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
D	PF05491	e7pbtD2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
D	PF17864	e7pbtD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
D	PF05496	e7pbtD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
E	PF05491	e7pbtE3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
E	PF17864	e7pbtE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
E	PF05496	e7pbtE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
F	PF05491	e7pbtF2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
F	PF17864	e7pbtF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
F	PF05496	e7pbtF3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF05496	ECOD (1.6)
G	PF07499	e7pbtG1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: PF07499	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF05491	RuvB C-terminal winged helix domain (RuvB_C)	RuvB C-terminal winged helix domain	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday j ...	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.	Domain
A, B, C, D, E A, B, C, D, E, F	PF05496	Holliday junction DNA helicase RuvB P-loop domain (RuvB_N)	Holliday junction DNA helicase RuvB P-loop domain	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday j ...	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This family contains the N-terminal region of the protein.	Domain
A, B, C, D, E A, B, C, D, E, F	PF17864	RuvB AAA lid domain (AAA_lid_4)	RuvB AAA lid domain	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday j ...	The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein [1]. This entry contains the AAA lid domain that is found to the C-terminus of the AAA domain.	Domain
G	PF07499	RuvA, C-terminal domain (RuvA_C)	RuvA, C-terminal domain	Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct d ...	Homologous recombination is a crucial process in all living organisms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB [1]. Within the Holliday junction, the C-terminal domain makes no interaction with DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Holliday junction ATP-dependent DNA helicase RuvB	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 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 four-way junction helicase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity 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 DNA secondary structure binding DNA binding four-way junction DNA binding nucleic acid binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination	protein-containing complex catalytic complex endodeoxyribonuclease complex Holliday junction resolvase complex intracellular protein-containing complex endonuclease complex intracellular anatomical structure cytoplasm cellular anatomical entity
G	Holliday junction ATP-dependent DNA helicase RuvA	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 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 four-way junction helicase activity DNA helicase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity DNA secondary structure binding DNA binding four-way junction DNA binding nucleic acid binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination	protein-containing complex catalytic complex DNA helicase complex Holliday junction helicase complex endodeoxyribonuclease complex Holliday junction resolvase complex intracellular protein-containing complex endonuclease complex intracellular anatomical structure cytoplasm cellular anatomical entity
H [auth U]	random DNA	-	-	-
I [auth V]	random DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008824	RuvB-like P-loop domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041445	RuvB, AAA lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004605	Holliday junction branch migration complex subunit RuvB	Family
A, B, C, D, E A, B, C, D, E, F	IPR008823	RuvB C-terminal winged helix domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G	IPR036267	RuvA, C-terminal domain superfamily	Homologous Superfamily
G	IPR011114	Holliday junction DNA helicase RuvA, C-terminal	Domain
G	IPR000085	Holliday junction branch migration complex subunit RuvA	Family
G	IPR010994	RuvA domain 2-like	Homologous Superfamily
G	IPR013849	DNA helicase, Holliday junction RuvA type, domain I, bacterial	Domain
G	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	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 R01GM133198.