5OG1 | pdb_00005og1

Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
F [auth A]SCOP2B SuperfamilyDouble Clp-N motif 8042763 3001383 SCOP2B (2022-06-29)
F [auth A]SCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)
E [auth B]SCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)
B [auth F]SCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyRecA-like P-loop NTPases 8039884 3002019 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
F [auth A]Sel1e5og1A1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)
E [auth B]Sel1e5og1B1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)
DSel1e5og1D1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)
C [auth E]Sel1e5og1E1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)
B [auth F]Sel1e5og1F1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)
A [auth C]Sel1e5og1C1 A: a/b three-layered sandwichesX: TIM beta/alpha-barrelH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: Sel1ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF10431C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)C-terminal, D2-small domain, of ClpB proteinThis 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
PF17871AAA lid domain (AAA_lid_9)AAA lid domainThis entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. Domain
PF02861Clp repeat (R) N-terminal domain (Clp_N)Clp repeat (R) N-terminal domain- Family
PF00004ATPase 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
PF07724AAA 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Chaperone protein ClpB,ATP-dependent Clp protease ATP-binding subunit ClpA,Chaperone protein ClpB

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR001270ClpA/B familyFamily
IPR018368ClpA/B, conserved site 1Conserved Site
IPR041546ClpA/ClpB, AAA lid domainDomain
IPR004176Clp, repeat (R) N-terminal domainDomain
IPR050130ATP-dependent Clp protease/Chaperone ClpA/ClpBFamily
IPR028299ClpA/B, conserved site 2Conserved Site
IPR003593AAA+ ATPase domainDomain
IPR003959ATPase, AAA-type, coreDomain
IPR013461ATP-dependent Clp protease ATP-binding subunit ClpAFamily
IPR019489Clp ATPase, C-terminalDomain
IPR036628Clp, N-terminal domain superfamilyHomologous Superfamily
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR001270ClpA/B familyFamily
IPR018368ClpA/B, conserved site 1Conserved Site
IPR041546ClpA/ClpB, AAA lid domainDomain
IPR004176Clp, repeat (R) N-terminal domainDomain
IPR050130ATP-dependent Clp protease/Chaperone ClpA/ClpBFamily
IPR028299ClpA/B, conserved site 2Conserved Site
IPR017730Chaperonin ClpBFamily
IPR003593AAA+ ATPase domainDomain
IPR003959ATPase, AAA-type, coreDomain
IPR019489Clp ATPase, C-terminalDomain
IPR036628Clp, N-terminal domain superfamilyHomologous Superfamily
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily