2YIU

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution

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: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101130	3000762	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c	8098502	3000815	SCOP2B (2022-06-29)
E	SCOP2 Family	Cytochrome bc1 domain	8098501	4000656	SCOP2 (2022-06-29)
E	SCOP2 Family	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101129	4002056	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Cytochrome c	8098502	3000815	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101130	3000762	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	ISP transmembrane anchor	8052876	3000753	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8052878	3000233	SCOP2B (2022-06-29)
F	SCOP2 Family	TAT signal-like	8044810	4004149	SCOP2 (2022-06-29)
F	SCOP2 Family	Rieske iron-sulfur protein (ISP)	8052877	4001667	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	ISP transmembrane anchor	8052876	3000753	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	ISP domain	8052878	3000233	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)
D	Cytochrom_B_C	e2yiuD3	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: Cytochrom_B_C	ECOD (1.6)
D	Cytochrome_B	e2yiuD2	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: Cytochrome_B	ECOD (1.6)
A	Cytochrom_B_C	e2yiuA3	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: Cytochrom_B_C	ECOD (1.6)
A	Cytochrome_B	e2yiuA1	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: Cytochrome_B	ECOD (1.6)
B	Cytochrom_C1_N	e2yiuB1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C1_N	ECOD (1.6)
E	Cytochrom_C1_N	e2yiuE1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrom_C1_N	ECOD (1.6)
C	Rieske_cytochrome_bc1	e2yiuC2	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_cytochrome_bc1	ECOD (1.6)
C	Rieske_6	e2yiuC3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_6	ECOD (1.6)
C	UCR_Fe-S_N	e2yiuC1	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: UCR_Fe-S_N	ECOD (1.6)
F	Rieske_cytochrome_bc1	e2yiuF8	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_cytochrome_bc1	ECOD (1.6)
F	Rieske_6	e2yiuF7	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_6	ECOD (1.6)
F	UCR_Fe-S_N	e2yiuF3	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: UCR_Fe-S_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
A	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
E	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
E	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
C	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
C	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
F	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00032	Cytochrome b(C-terminal)/b6/petD (Cytochrom_B_C)	Cytochrome b(C-terminal)/b6/petD	-	Domain
A, D	PF00033	Cytochrome b/b6/petB (Cytochrome_B)	Cytochrome b/b6/petB	-	Domain
B, E	PF02167	Cytochrome C1 family (Cytochrom_C1)	Cytochrome C1 family	-	Family
C, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	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 cellular metabolic process 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 cellular anatomical entity transporter complex respiratory chain complex III transmembrane transporter complex oxidoreductase complex cell periphery plasma membrane
B, E	CYTOCHROME C1, HEME PROTEIN	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cell periphery plasma membrane membrane cellular anatomical entity
C, F	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 plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex III (bc1 and b6f) superfamily	Cytochrome bc1 and b6f complexes

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

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.