7MR3

Cryo-EM structure of RecBCD-DNA complex with docked RecBNuc and stabilized RecD

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)
C [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043249	3002019	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043248	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Restriction endonuclease-like	8043244	3000104	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043242	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043241	3002019	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Restriction endonuclease-like	8043247	3000104	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043245	3002019	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043246	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)
C [auth D]	F_UNCLASSIFIED	e7mr3D4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth D]	recD	e7mr3D3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: recD	ECOD (1.6)
C [auth D]	AAA_19	e7mr3D2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_19	ECOD (1.6)
C [auth D]	UvrD_C_2	e7mr3D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C_2	ECOD (1.6)
A [auth B]	UvrD-helicase	e7mr3B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD-helicase	ECOD (1.6)
A [auth B]	UvrD_C	e7mr3B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C	ECOD (1.6)
A [auth B]	PDDEXK_1	e7mr3B2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: PDDEXK_1	ECOD (1.6)
B [auth C]	UvrD_C	e7mr3C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: UvrD_C	ECOD (1.6)
B [auth C]	Exonuc_V_gamma	e7mr3C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Exonuc_V_gamma	ECOD (1.6)
B [auth C]	recC	e7mr3C3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: recC	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D]	PF13538	UvrD-like helicase C-terminal domain (UvrD_C_2)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
C [auth D]	PF21185	RecBCD enzyme subunit RecD, N-terminal domain (RecD_N)	RecBCD enzyme subunit RecD, N-terminal domain	This domain is found in RecBCD enzyme subunit RecD from Escherichia coli and in similar proteins mostly found in Gammaproteobacteria. RecD is a 5'-3' helicase that comprises three domains. This entry represents the N-terminal domain of RecD, which fo ...	This domain is found in RecBCD enzyme subunit RecD from Escherichia coli and in similar proteins mostly found in Gammaproteobacteria. RecD is a 5'-3' helicase that comprises three domains. This entry represents the N-terminal domain of RecD, which forms the principal interface between RecD and domain 2B of RecC and leads to the conformational change in RecD that has significant effects on the conformation of the RecC subunit [1-4].	Domain
C [auth D]	PF13245	AAA domain (AAA_19)	AAA domain	-	Domain
A [auth B]	PF13361	UvrD-like helicase C-terminal domain (UvrD_C)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
A [auth B]	PF00580	UvrD/REP helicase N-terminal domain (UvrD-helicase)	UvrD/REP helicase N-terminal domain	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near t ...	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.	Domain
B [auth C]	PF04257	Exodeoxyribonuclease V, gamma subunit (Exonuc_V_gamma)	Exodeoxyribonuclease V, gamma subunit	-	Family
B [auth C]	PF17946	RecC C-terminal domain (RecC_C)	RecC C-terminal domain	This entry corresponds to the C-terminal domain of the RecC protein. This domain has a PD(D/E)XK like fold. Deleting this domain eliminates RecD assembly within the RecBCD complex [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	RecBCD enzyme subunit RecD	ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity 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 DNA binding nucleic acid binding DNA exonuclease activity hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity isomerase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides single-stranded DNA helicase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process recombinational repair metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair	protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
D [auth X]	DNA (60-MER)	-	-	-
A [auth B]	RecBCD enzyme subunit RecB	DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity DNA endonuclease activity endonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity DNA endonuclease activity endonuclease activity ATP-dependent activity, acting on DNA ATP-dependent activity DNA helicase activity helicase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding DNA translocase activity isomerase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides 3'-5' DNA helicase activity	response to stimulus response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair cellular response to stress response to stimulus response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to external biotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
B [auth C]	RecBCD enzyme subunit RecC	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 DNA binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity ATP-dependent activity, acting on DNA DNA helicase activity helicase activity ATP-dependent activity	cellular response to stimulus double-strand break repair 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 cellular response to stimulus double-strand break repair 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 double-strand break repair via homologous recombination DNA repair response to radiation response to abiotic stimulus biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to external biotic stimulus	protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
E [auth A]	DNA (60-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR050534	Coronaviruses polyprotein 1ab	Family
C [auth D]	IPR006344	RecBCD enzyme subunit RecD	Family
C [auth D]	IPR049550	RecBCD enzyme subunit RecD, N-terminal domain	Domain
C [auth D]	IPR003593	AAA+ ATPase domain	Domain
C [auth D]	IPR027785	UvrD-like helicase C-terminal domain	Domain
C [auth D]	IPR041851	RecBCD enzyme subunit RecD, N-terminal domain superfamily	Homologous Superfamily
C [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR014017	UvrD-like DNA helicase, C-terminal	Domain
A [auth B]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A [auth B]	IPR004586	RecBCD enzyme subunit RecB	Family
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR038726	PD-(D/E)XK endonuclease-like domain, AddAB-type	Domain
A [auth B]	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
A [auth B]	IPR014016	UvrD-like helicase, ATP-binding domain	Domain
A [auth B]	IPR000212	DNA helicase, UvrD/REP type	Family
B [auth C]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
B [auth C]	IPR006697	RecBCD enzyme subunit RecC	Family
B [auth C]	IPR041500	RecC, C-terminal	Domain
B [auth C]	IPR013986	DExx box DNA helicase domain superfamily	Homologous Superfamily
B [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily