7X7Q | pdb_00007x7q

CryoEM structure of RuvA-RuvB-Holliday junction complex

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	F_UNCLASSIFIED	e7x7qA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e7x7qA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e7x7qA3	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: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e7x7qB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e7x7qB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e7x7qC2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e7x7qC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e7x7qD3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e7x7qD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
D	F_UNCLASSIFIED	e7x7qD2	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: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e7x7qE2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e7x7qE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e7x7qF3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e7x7qF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e7x7qF2	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: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e7x7qG2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e7x7qG1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
H	F_UNCLASSIFIED	e7x7qH1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
H	F_UNCLASSIFIED	e7x7qH3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)
H	F_UNCLASSIFIED	e7x7qH2	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: F_UNCLASSIFIED	ECOD (1.6)
I [auth M]	F_UNCLASSIFIED	e7x7qM3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
I [auth M]	F_UNCLASSIFIED	e7x7qM1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: F_UNCLASSIFIED	ECOD (1.6)
I [auth M]	F_UNCLASSIFIED	e7x7qM2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth N]	F_UNCLASSIFIED	e7x7qN2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth N]	F_UNCLASSIFIED	e7x7qN3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth N]	F_UNCLASSIFIED	e7x7qN1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth O]	F_UNCLASSIFIED	e7x7qO2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth O]	F_UNCLASSIFIED	e7x7qO3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth O]	F_UNCLASSIFIED	e7x7qO1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
L [auth P]	F_UNCLASSIFIED	e7x7qP2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
L [auth P]	F_UNCLASSIFIED	e7x7qP3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: F_UNCLASSIFIED	ECOD (1.6)
L [auth P]	F_UNCLASSIFIED	e7x7qP1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	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, G, H	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
A, B, C, D, E A, B, C, D, E, F, G, H	PF01330	RuvA N terminal domain (RuvA_N)	RuvA N terminal domain	The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain		Domain
I [auth M], J [auth N], K [auth O], L [auth P]	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
I [auth M], J [auth N], K [auth O], L [auth P]	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
I [auth M], J [auth N], K [auth O], L [auth P]	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	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, G, H	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 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 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 SOS response 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 SOS response 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 cellular anatomical structure intracellular anatomical structure cytoplasm
I [auth M], J [auth N], K [auth O], L [auth P]	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 cellular response to chemical stimulus cellular response to chromate response to stimulus response to chemical response to chromate response to oxygen-containing compound cellular process cellular response to oxygen-containing compound primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress cellular response to stimulus cellular response to chemical stimulus cellular response to chromate response to stimulus response to chemical response to chromate response to oxygen-containing compound cellular process cellular response to oxygen-containing compound 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 macromolecule metabolic process DNA repair response to selenite ion cellular response to selenite ion 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
M [auth I]	DNA (40-MER)	-	-	-
N [auth K]	DNA (40-MER)	-	-	-
O [auth J]	DNA (26-MER)	-	-	-
P [auth L]	DNA (26-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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