7ZXY | pdb_00007zxy

3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Synechocystis sp. PCC 6803 with natively bound plastoquinone and lipid molecules.

External Resource: Annotation

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: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
P	Glycos_transf_N	e7zxyP1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
H	Glycos_transf_N	e7zxyH1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
O	Glycos_transf_N	e7zxyO1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
G	Glycos_transf_N	e7zxyG1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
N	Glycos_transf_N	e7zxyN1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
F	Glycos_transf_N	e7zxyF1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
L	Glycos_transf_N	e7zxyL2	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
D	Glycos_transf_N	e7zxyD1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
K	Glycos_transf_N	e7zxyK1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
C	Glycos_transf_N	e7zxyC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
J	Glycos_transf_N	e7zxyJ1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
B	Glycos_transf_N	e7zxyB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
I	Glycos_transf_N	e7zxyI1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)
A	Glycos_transf_N	e7zxyA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Glycos_transf_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)
A	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
H, P	PF03742	PetN (PetN)	PetN	-	Family
G, O	PF02529	Cytochrome B6-F complex subunit 5 (PetG)	Cytochrome B6-F complex subunit 5	-	Family
F, N	PF08041	PetM family of cytochrome b6f complex subunit 7 (PetM)	PetM family of cytochrome b6f complex subunit 7	-	Family
D, L	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
C, K	PF16639	Apocytochrome F, N-terminal (Apocytochr_F_N)	Apocytochrome F, N-terminal	This is the N-terminal domain of cytochrome f. It is a soluble lumen-side domain [1].	Domain
C, K	PF01333	Apocytochrome F, C-terminal (Apocytochr_F_C)	Apocytochrome F, C-terminal	This is a sub-family of cytochrome C. See Pfam:PF00034.	Domain
B, J	PF00032	Cytochrome b(C-terminal)/b6/petD (Cytochrom_B_C)	Cytochrome b(C-terminal)/b6/petD		Domain
A, I	PF00033	Cytochrome b/b6/petB (Cytochrome_B)	Cytochrome b/b6/petB		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H, P	Cytochrome b6-f complex subunit 8	electron transfer activity	photosynthesis metabolic process cellular process cytochrome complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane
G, O	Cytochrome b6-f complex subunit 5	-	photosynthesis metabolic process cellular process cytochrome complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane
F, N	Cytochrome b6-f complex subunit 7	electron transfer activity	photosynthesis metabolic process cellular process	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane
E, M	Cytochrome B6	-	-	-
D, L	Cytochrome b6-f complex iron-sulfur subunit 2	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity electron transfer activity plastoquinol--plastocyanin reductase activity oxidoreduction-driven active transmembrane transporter activity oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity electron transfer activity plastoquinol--plastocyanin reductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity oxidoreductase activity, acting on diphenols and related substances as donors, with copper protein as acceptor transporter activity transmembrane transporter activity cation binding ion binding metal ion binding	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid
C, K	Cytochrome f	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis metabolic process cellular process	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane
B, J	Cytochrome b6-f complex subunit 4	oxidoreductase activity catalytic activity electron transfer activity	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane
A, I	Cytochrome b6	oxidoreductase activity catalytic activity electron transfer 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 photosynthesis	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex intracellular membraneless organelle intracellular organelle cellular anatomical structure cytochrome b6f complex organelle membraneless organelle thylakoid plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H, P	IPR036143	Cytochrome b6-f complex, subunit 8 superfamily	Homologous Superfamily
H, P	IPR005497	Cytochrome b6-f complex, subunit 8	Family
G, O	IPR003683	Cytochrome b6/f complex, subunit 5	Family
G, O	IPR036099	Cytochrome b6/f complex, subunit 5 superfamily	Homologous Superfamily
F, N	IPR012595	PetM of cytochrome b6/f complex subunit 7	Family
D, L	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
D, L	IPR000595	Cyclic nucleotide-binding domain	Domain
D, L	IPR014349	Rieske iron-sulphur protein	Family
D, L	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
D, L	IPR005805	Rieske iron-sulphur protein, C-terminal	Domain
D, L	IPR023960	Cytochrome b6-f complex iron-sulfur subunit	Family
D, L	IPR057415	Cytochrome b6-f complex iron-sulfur subunit-like, transmembrane anchor	Domain
C, K	IPR002325	Cytochrome f	Family
C, K	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
C, K	IPR036826	Cytochrome f large domain superfamily	Homologous Superfamily
C, K	IPR024058	Cytochrome f transmembrane anchor	Homologous Superfamily
C, K	IPR024094	Cytochrome f large domain	Domain
B, J	IPR036150	Cytochrome b/b6, C-terminal domain superfamily	Homologous Superfamily
B, J	IPR005798	Cytochrome b/b6, C-terminal	Domain
B, J	IPR005870	Cytochrome b6/f complex, subunit IV	Family
B, J	IPR048260	Cytochrome b/b6, C-terminal domain, eukaryotic/bacterial	Domain
A, I	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
A, I	IPR023530	Cytochrome b6, PetB	Family
A, I	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
A, I	IPR048259	Cytochrome b/b6, N-terminal domain, eukaryotic/bacterial	Domain
A, I	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, F A, B, C, D, F, G, H, I, J, K, L, N, O, P	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, F A, B, C, D, F, G, H, I, J, K, L, N, O, P	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, F A, B, C, D, F, G, H, I, J, K, L, N, O, P	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Cytochrome b₆f of Oxygenic Photosynthesis	Dimeric cytochrome b6f-PetP complex