1QVR | pdb_00001qvr

Crystal Structure Analysis of ClpB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	d1qvrc1	All alpha proteins	Double Clp-N motif	Double Clp-N motif	Double Clp-N motif	N-terminal domain of ClpB (heat shock protein F84.1)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1qvrc3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1qvrc2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1qvrb1	All alpha proteins	Double Clp-N motif	Double Clp-N motif	Double Clp-N motif	N-terminal domain of ClpB (heat shock protein F84.1)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1qvrb3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1qvrb2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, N-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1qvra1	All alpha proteins	Double Clp-N motif	Double Clp-N motif	Double Clp-N motif	N-terminal domain of ClpB (heat shock protein F84.1)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1qvra3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, C-terminal domain	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1qvra2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Extended AAA-ATPase domain	ClpB, AAA+ modules, N-terminal domain	(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)
C	SCOP2B Superfamily	Double Clp-N motif	8040002	3001383	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8040005	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8040004	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104154	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8040004	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Double Clp-N motif	8040002	3001383	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104154	3002834	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8040005	3002019	SCOP2B (2022-06-29)
A	SCOP2 Family	Double Clp-N motif	8027623	4002527	SCOP2 (2022-06-29)
A	SCOP2 Family	Extended AAA-ATPase domain	8027625	4000283	SCOP2 (2022-06-29)
A	SCOP2 Family	Extended AAA-ATPase domain	8027626	4000283	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Double Clp-N motif	8040002	3001383	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8040004	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8040005	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA polymerases epsilon, N-terminal domain (Dpoe2NT)-like	8104154	3002834	SCOP2 (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	Clp_N	e1qvrC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: double Clp-N	F: Clp_N	ECOD (1.6)
C	ClpB_D2-small	e1qvrC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
C	chaperone_ClpB	e1qvrC3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: chaperone_ClpB	ECOD (1.6)
C	Sigma54_activat	e1qvrC5	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)
B	Clp_N	e1qvrB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: double Clp-N	F: Clp_N	ECOD (1.6)
B	ClpB_D2-small	e1qvrB8	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
B	chaperone_ClpB	e1qvrB7	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: chaperone_ClpB	ECOD (1.6)
B	Sigma54_activat	e1qvrB6	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)
A	Clp_N	e1qvrA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: double Clp-N	F: Clp_N	ECOD (1.6)
A	ClpB_D2-small	e1qvrA8	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: ClpB_D2-small	ECOD (1.6)
A	chaperone_ClpB	e1qvrA7	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: chaperone_ClpB	ECOD (1.6)
A	Sigma54_activat	e1qvrA6	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)
C	1.10.1780.10	Mainly Alpha	Orthogonal Bundle	Double Clp-N motif	Clp, N-terminal domain	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	6.10.140.130	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.10.1780.10	Mainly Alpha	Orthogonal Bundle	Double Clp-N motif	Clp, N-terminal domain	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.1780.10	Mainly Alpha	Orthogonal Bundle	Double Clp-N motif	Clp, N-terminal domain	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF10431	C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)	C-terminal, D2-small domain, of ClpB protein	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 ...	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.	Domain
A, B, C	PF17871	AAA lid domain (AAA_lid_9)	AAA lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C	PF02861	Clp repeat (R) N-terminal domain (Clp_N)	Clp repeat (R) N-terminal domain	-	Family
A, B, C	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
A, B, C	PF07724	AAA domain (Cdc48 subfamily) (AAA_2)	AAA domain (Cdc48 subfamily)	This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	ClpB protein	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 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 catalytic activity ATP-dependent activity identical protein binding protein binding	protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to heat response to stimulus protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001270	ClpA/B family	Family
A, B, C	IPR018368	ClpA/B, conserved site 1	Conserved Site
A, B, C	IPR041546	ClpA/ClpB, AAA lid domain	Domain
A, B, C	IPR004176	Clp, repeat (R) N-terminal domain	Domain
A, B, C	IPR050130	ATP-dependent Clp protease/Chaperone ClpA/ClpB	Family
A, B, C	IPR028299	ClpA/B, conserved site 2	Conserved Site
A, B, C	IPR017730	Chaperonin ClpB	Family
A, B, C	IPR003593	AAA+ ATPase domain	Domain
A, B, C	IPR003959	ATPase, AAA-type, core	Domain
A, B, C	IPR019489	Clp ATPase, C-terminal	Domain
A, B, C	IPR036628	Clp, N-terminal domain superfamily	Homologous Superfamily
A, B, 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.