1BDX | pdb_00001bdx

E. COLI DNA HELICASE RUVA WITH BOUND DNA HOLLIDAY JUNCTION, ALPHA CARBONS AND PHOSPHATE ATOMS ONLY

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d1bdxa1	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	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
E [auth A]	d1bdxa2	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
E [auth A]	d1bdxa3	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
G [auth C]	d1bdxc1	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	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
G [auth C]	d1bdxc2	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
G [auth C]	d1bdxc3	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
H [auth D]	d1bdxd1	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	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
H [auth D]	d1bdxd2	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
H [auth D]	d1bdxd3	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
F [auth B]	d1bdxb1	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	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
F [auth B]	d1bdxb2	All alpha proteins	SAM domain-like	RuvA domain 2-like	DNA helicase RuvA subunit, middle domain	DNA helicase RuvA subunit, middle domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
F [auth B]	d1bdxb3	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA helicase RuvA subunit, N-terminal domain	DNA helicase RuvA subunit, N-terminal domain	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037705	3000163	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041920	3000135	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	DNA helicase RuvA subunit, C-terminal domain	8036671	3001225	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041920	3000135	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	DNA helicase RuvA subunit, C-terminal domain	8036671	3001225	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037705	3000163	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041920	3000135	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	DNA helicase RuvA subunit, C-terminal domain	8036671	3001225	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037705	3000163	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	DNA helicase RuvA subunit, C-terminal domain	8036671	3001225	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041920	3000135	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Helix-hairpin-helix tandem	8037705	3000163	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)
E [auth A]	Stap_Strp_toxin	e1bdxA1	A: beta barrels	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.2)
E [auth A]	IMS_HHH_1	e1bdxA2	A: beta barrels	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.2)
E [auth A]	PS-DH	e1bdxA3	A: beta barrels	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PS-DH	ECOD (v294.2)
G [auth C]	Stap_Strp_toxin	e1bdxC1	A: beta barrels	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.2)
G [auth C]	IMS_HHH_1	e1bdxC2	A: beta barrels	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.2)
G [auth C]	PS-DH	e1bdxC3	A: beta barrels	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PS-DH	ECOD (v294.2)
H [auth D]	Stap_Strp_toxin	e1bdxD1	A: beta barrels	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.2)
H [auth D]	IMS_HHH_1	e1bdxD2	A: beta barrels	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.2)
H [auth D]	PS-DH	e1bdxD3	A: beta barrels	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PS-DH	ECOD (v294.2)
F [auth B]	Stap_Strp_toxin	e1bdxB1	A: beta barrels	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.2)
F [auth B]	IMS_HHH_1	e1bdxB2	A: beta barrels	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.2)
F [auth B]	PS-DH	e1bdxB3	A: beta barrels	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: PS-DH	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B], G [auth C], H [auth D]	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
E [auth A], F [auth B], G [auth C], H [auth D]	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
E [auth A], F [auth B], G [auth C], H [auth D]	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B], G [auth C], H [auth D]	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 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 identical protein binding protein binding	cellular response to stimulus response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus DNA recombination 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 recombinational repair metabolic process cellular process macromolecule metabolic process DNA repair response to radiation response to abiotic stimulus SOS response	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
A [auth J], B [auth K], C [auth L], D [auth M]	DNA (5'-D(PGPCPAPTPGPCPAPTPAPTPGPCPAPTPGPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth C], H [auth D]	IPR036267	RuvA, C-terminal domain superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR011114	Holliday junction DNA helicase RuvA, C-terminal	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR000085	Holliday junction branch migration complex subunit RuvA	Family
E [auth A], F [auth B], G [auth C], H [auth D]	IPR010994	RuvA domain 2-like	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR013849	DNA helicase, Holliday junction RuvA type, domain I, bacterial	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth D]	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.