Annotations: 1IXR

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ixra1	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1ixra2	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1ixrb1	All alpha proteins	RuvA C-terminal domain-like	DNA helicase RuvA subunit, C-terminal domain	DNA helicase RuvA subunit, C-terminal domain	DNA helicase RuvA subunit, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1ixrb2	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1ixrb3	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1ixrc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Helicase DNA-binding domain	Holliday junction helicase RuvB	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1ixrc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	Holliday junction helicase RuvB	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DNA helicase RuvA subunit, middle domain	8030187	4001026	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA helicase RuvA subunit, N-terminal domain	8030188	4001893	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helix-hairpin-helix tandem	8042566	3000163	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8042567	3000135	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DNA helicase RuvA subunit, C-terminal domain	8042572	3001225	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8042567	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helix-hairpin-helix tandem	8042566	3000163	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8058580	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104163	3002834	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8058578	3002019	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)
A	RuvA_N	e1ixrA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RuvA_N	ECOD (1.6)
A	HHH_5	e1ixrA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
B	RuvA_N	e1ixrB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RuvA_N	ECOD (1.6)
B	HHH_5	e1ixrB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
B	RuvA_C	e1ixrB3	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: RuvA_C	ECOD (1.6)
C	RuvB_C	e1ixrC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: RuvB_C	ECOD (1.6)
C	RuvB_N	e1ixrC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: RuvB_N	ECOD (1.6)
C	Sigma54_activat	e1ixrC3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain	-	Domain
C	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
C	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
C	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, B	Holliday junction 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 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
C	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 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

InterPro: Protein Family Classification InterPro Database Homepage

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