8EFV

Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
A [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	DNA polymerases epsilon N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	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)
B [auth C]	PF05491	e8efvC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
B [auth C]	PF17864	e8efvC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
B [auth C]	PF05496	e8efvC3	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 [auth F]	PF05491	e8efvF3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
E [auth F]	PF17864	e8efvF2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
E [auth F]	PF05496	e8efvF1	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 [auth E]	PF05491	e8efvE1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
F [auth E]	PF17864	e8efvE2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
F [auth E]	PF05496	e8efvE3	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)
A [auth D]	PF05491	e8efvD2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
A [auth D]	PF17864	e8efvD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
A [auth D]	PF05496	e8efvD1	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 [auth B]	PF05491	e8efvB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
C [auth B]	PF17864	e8efvB3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
C [auth B]	PF05496	e8efvB2	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 [auth A]	PF05491	e8efvA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
D [auth A]	PF17864	e8efvA3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
D [auth A]	PF05496	e8efvA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	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 [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	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 [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	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
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	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	49-mer DNA	-	-	-
H	51-mer DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR008824	RuvB-like P-loop domain	Domain
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR041445	RuvB, AAA lid domain	Domain
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR003593	AAA+ ATPase domain	Domain
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR004605	Holliday junction branch migration complex subunit RuvB	Family
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	IPR008823	RuvB C-terminal winged helix domain	Domain
A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	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 R01GM133198.