2YIU | pdb_00002yiu

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
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)
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)
C	SCOP2B Superfamily	ISP transmembrane anchor	8052876	3000753	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8052878	3000233	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Pyridoxal_deC	e2yiuF7	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Pyridoxal_deC	ECOD (v294.1)
F	Toxin_R_bind_N	e2yiuF3	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Toxin_R_bind_N	ECOD (v294.1)
C	RPOC_hybrid	e2yiuC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RPOC_hybrid	ECOD (v294.1)
C	MoCoBD_2	e2yiuC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MoCoBD_2	ECOD (v294.1)
E	Cytochrom_C1	e2yiuE1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Cytochrom_C1	ECOD (v294.1)
B	Cytochrom_C1	e2yiuB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: Cytochrom_C1	ECOD (v294.1)
D		e2yiuD2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F:	ECOD (v294.1)
D	Peptidase_S8	e2yiuD3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (v294.1)
A	PDH_N, F420_oxidored	e2yiuA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: Cystatin/monellin	T: Cystatin/monellin	F: PDH_N, F420_oxidored	ECOD (v294.1)
A	GMC_oxred_C	e2yiuA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: GMC_oxred_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	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)
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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter 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, E	CYTOCHROME C1, HEME PROTEIN	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
A, D	CYTOCHROME B	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter 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 cellular anatomical structure cytochrome complex catalytic complex transmembrane transporter complex membrane membrane protein complex transporter complex respiratory chain complex III cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B, E	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, E	IPR002326	Cytochrome c1	Family
B, E	IPR009056	Cytochrome c-like domain	Domain
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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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