7PBR | pdb_00007pbr

RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s0-A [t2 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)
F	RuvB_C	e7pbrF1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
F	RuvB_N	e7pbrF2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
F	Sigma54_activat	e7pbrF3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
E	RuvB_C	e7pbrE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
E	RuvB_N	e7pbrE3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
E	Sigma54_activat	e7pbrE2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
D	RuvB_C	e7pbrD3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
D	RuvB_N	e7pbrD2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
D	Sigma54_activat	e7pbrD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
C	RuvB_C	e7pbrC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
C	RuvB_N	e7pbrC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
C	Sigma54_activat	e7pbrC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
B	RuvB_C	e7pbrB3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
B	RuvB_N	e7pbrB2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
B	Sigma54_activat	e7pbrB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	ECOD (1.6)
A	RuvB_C	e7pbrA3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
A	RuvB_N	e7pbrA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
A	Sigma54_activat	e7pbrA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma54_activat	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 (WHD_RuvB)	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth V]	random DNA	-	-	-
G [auth U]	random DNA	-	-	-
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 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 nucleic acid conformation isomerase activity four-way junction helicase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity macromolecular conformation isomerase 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 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 cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008824	RuvB-like, AAA+ ATPase domain	Domain
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	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	IPR008823	RuvB, winged helix, C-terminal 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	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.