7X7Q

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)
D	PF01330	e7x7qD3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
D	PF14520	e7x7qD1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
D	PF07499	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: PF07499	ECOD (1.6)
A	PF01330	e7x7qA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
A	PF14520	e7x7qA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
A	PF07499	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: PF07499	ECOD (1.6)
B	PF01330	e7x7qB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
B	PF14520	e7x7qB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
C	PF01330	e7x7qC2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
C	PF14520	e7x7qC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
E	PF01330	e7x7qE2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
E	PF14520	e7x7qE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
F	PF01330	e7x7qF3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
F	PF14520	e7x7qF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
F	PF07499	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: PF07499	ECOD (1.6)
G	PF01330	e7x7qG2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
G	PF14520	e7x7qG1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
H	PF01330	e7x7qH1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01330	ECOD (1.6)
H	PF14520	e7x7qH3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF14520	ECOD (1.6)
H	PF07499	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: PF07499	ECOD (1.6)
J [auth N]	PF05491	e7x7qN2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
J [auth N]	PF17864	e7x7qN3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
J [auth N]	PF05496	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: PF05496	ECOD (1.6)
I [auth M]	PF05491	e7x7qM3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
I [auth M]	PF17864	e7x7qM1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
I [auth M]	PF05496	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: PF05496	ECOD (1.6)
K [auth O]	PF05491	e7x7qO2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
K [auth O]	PF17864	e7x7qO3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
K [auth O]	PF05496	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: PF05496	ECOD (1.6)
L [auth P]	PF05491	e7x7qP2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05491	ECOD (1.6)
L [auth P]	PF17864	e7x7qP3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17864	ECOD (1.6)
L [auth P]	PF05496	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: PF05496	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 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
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 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 cellular response to inorganic substance cellular response to chromate response to stimulus response to chromate response to oxygen-containing compound cellular response to oxygen-containing compound response to inorganic substance cellular response to chemical stimulus response to chemical cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process cellular response to stimulus cellular response to inorganic substance cellular response to chromate response to stimulus response to chromate response to oxygen-containing compound cellular response to oxygen-containing compound response to inorganic substance cellular response to chemical stimulus response to chemical cellular process 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 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 intracellular anatomical structure cytoplasm cellular anatomical entity
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]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
I [auth M], J [auth N], K [auth O], L [auth P]	IPR008824	RuvB-like P-loop domain	Domain
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]	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]	IPR008823	RuvB C-terminal winged helix domain	Domain
I [auth M], J [auth N], K [auth O], L [auth P]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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7X7Q

CryoEM structure of RuvA-RuvB-Holliday junction complex

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage