8ASJ

Four subunit cytochrome b-c1 complex from Rhodobacter sphaeroides in native nanodiscs - focussed refinement in the b-c conformation

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cytochrome c	8099394	3000815	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101134	3000762	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101134	3000762	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cytochrome c	8099394	3000815	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	F_UNCLASSIFIED	e8asjA2	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8asjA1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e8asjA3	A: extended segments	X: iron-sulfur subunit (ISP) transmembrane anchor (From Topology)	H: iron-sulfur subunit (ISP) transmembrane anchor (From Topology)	T: iron-sulfur subunit (ISP) transmembrane anchor	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8asjE3	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8asjE2	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e8asjE1	A: extended segments	X: iron-sulfur subunit (ISP) transmembrane anchor (From Topology)	H: iron-sulfur subunit (ISP) transmembrane anchor (From Topology)	T: iron-sulfur subunit (ISP) transmembrane anchor	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8asjB2	A: alpha bundles	X: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) (From Topology)	H: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) (From Topology)	T: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e8asjB1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8asjF2	A: alpha bundles	X: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) (From Topology)	H: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) (From Topology)	T: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	F: F_UNCLASSIFIED	ECOD (1.6)
F	F_UNCLASSIFIED	e8asjF1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle (From Homology)	H: Transmembrane heme-binding four-helical bundle	T: Transmembrane di-heme cytochromes	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e8asjC1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e8asjG1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (utative)
B	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)
F	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF00355	Rieske [2Fe-2S] domain (Rieske)	Rieske [2Fe-2S] domain	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].	Domain
B, F	PF00032	Cytochrome b(C-terminal)/b6/petD (Cytochrom_B_C)	Cytochrome b(C-terminal)/b6/petD		Domain
B, F	PF00033	Cytochrome b/b6/petB (Cytochrome_B)	Cytochrome b/b6/petB		Domain
C, G	PF02167	Cytochrome C1 family (Cytochrom_C1)	Cytochrome C1 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Ubiquinol-cytochrome c reductase iron-sulfur subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity ubiquinol-cytochrome-c reductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity ubiquinol-cytochrome-c reductase activity catalytic activity transmembrane transporter activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	cell periphery cellular anatomical structure plasma membrane membrane
B, F	Cytochrome b	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity ubiquinol-cytochrome-c reductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity oxidoreductase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity ubiquinol-cytochrome-c reductase activity catalytic activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	respiratory chain complex protein-containing complex catalytic complex cytochrome complex membrane membrane protein complex transporter complex respiratory chain complex III cellular anatomical structure transmembrane transporter complex oxidoreductase complex
C, G	Cytochrome c1	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cellular anatomical structure membrane
D, H	Cytochrome b-c1 subunit IV	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
A, E	IPR005805	Rieske iron-sulphur protein, C-terminal	Domain
A, E	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
A, E	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A, E	IPR014349	Rieske iron-sulphur protein	Family
A, E	IPR019470	Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal	Domain
A, E	IPR006317	Ubiquinol-cytochrome c reductase, iron-sulphur subunit	Domain
A, E	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
B, F	IPR036150	Cytochrome b/b6, C-terminal domain superfamily	Homologous Superfamily
B, F	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
B, F	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
B, F	IPR005798	Cytochrome b/b6, C-terminal	Domain
B, F	IPR048259	Cytochrome b/b6, N-terminal domain, eukaryotic/bacterial	Domain
B, F	IPR030689	Cytochrome b	Family
B, F	IPR048260	Cytochrome b/b6, C-terminal domain, eukaryotic/bacterial	Domain
B, F	IPR005797	Cytochrome b/b6, N-terminal domain	Domain
C, G	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
C, G	IPR002326	Cytochrome c1	Family
C, G	IPR009056	Cytochrome c-like domain	Domain

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H	PDBTM	Annotated as membrane protein by PDBTM

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.