7ZXY

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
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)
A	PF00033	e7zxyA1	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: PF00033	ECOD (1.6)
I	PF00033	e7zxyI1	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: PF00033	ECOD (1.6)
B	PF00032	e7zxyB1	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: PF00032	ECOD (1.6)
J	PF00032	e7zxyJ1	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: PF00032	ECOD (1.6)
C	PF16639	e7zxyC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: PF16639	ECOD (1.6)
C	PF01333	e7zxyC3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PF01333	ECOD (1.6)
C	PF01333	e7zxyC1	A: extended segments	X: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor (From Topology)	H: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor (From Topology)	T: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor	F: PF01333	ECOD (1.6)
K	PF16639	e7zxyK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: PF16639	ECOD (1.6)
K	PF01333	e7zxyK3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PF01333	ECOD (1.6)
K	PF01333	e7zxyK2	A: extended segments	X: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor (From Topology)	H: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor (From Topology)	T: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor	F: PF01333	ECOD (1.6)
D	F_UNCLASSIFIED	e7zxyD2	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF00355	e7zxyD1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF00355	ECOD (1.6)
D	F_UNCLASSIFIED	e7zxyD3	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)
L	F_UNCLASSIFIED	e7zxyL1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: F_UNCLASSIFIED	ECOD (1.6)
L	PF00355	e7zxyL3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: PF00355	ECOD (1.6)
L	F_UNCLASSIFIED	e7zxyL2	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	e7zxyE1	A: extended segments	X: PetL subunit of the cytochrome b6f complex (From Topology)	H: PetL subunit of the cytochrome b6f complex (From Topology)	T: PetL subunit of the cytochrome b6f complex	F: F_UNCLASSIFIED	ECOD (1.6)
M	F_UNCLASSIFIED	e7zxyM1	A: extended segments	X: PetL subunit of the cytochrome b6f complex (From Topology)	H: PetL subunit of the cytochrome b6f complex (From Topology)	T: PetL subunit of the cytochrome b6f complex	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF08041	e7zxyF1	A: extended segments	X: PetM subunit of the cytochrome b6f complex (From Topology)	H: PetM subunit of the cytochrome b6f complex (From Topology)	T: PetM subunit of the cytochrome b6f complex	F: PF08041	ECOD (1.6)
N	PF08041	e7zxyN1	A: extended segments	X: PetM subunit of the cytochrome b6f complex (From Topology)	H: PetM subunit of the cytochrome b6f complex (From Topology)	T: PetM subunit of the cytochrome b6f complex	F: PF08041	ECOD (1.6)
G	PF02529	e7zxyG1	A: extended segments	X: PetG subunit of the cytochrome b6f complex (From Topology)	H: PetG subunit of the cytochrome b6f complex (From Topology)	T: PetG subunit of the cytochrome b6f complex	F: PF02529	ECOD (1.6)
O	PF02529	e7zxyO1	A: extended segments	X: PetG subunit of the cytochrome b6f complex (From Topology)	H: PetG subunit of the cytochrome b6f complex (From Topology)	T: PetG subunit of the cytochrome b6f complex	F: PF02529	ECOD (1.6)
H	PF03742	e7zxyH1	A: extended segments	X: PetN subunit of the cytochrome b6f complex (From Topology)	H: PetN subunit of the cytochrome b6f complex (From Topology)	T: PetN subunit of the cytochrome b6f complex	F: PF03742	ECOD (1.6)
P	PF03742	e7zxyP1	A: extended segments	X: PetN subunit of the cytochrome b6f complex (From Topology)	H: PetN subunit of the cytochrome b6f complex (From Topology)	T: PetN subunit of the cytochrome b6f complex	F: PF03742	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, I	PF00033	Cytochrome b/b6/petB (Cytochrome_B)	Cytochrome b/b6/petB	-	Domain
B, J	PF00032	Cytochrome b(C-terminal)/b6/petD (Cytochrom_B_C)	Cytochrome b(C-terminal)/b6/petD	-	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
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
F, N	PF08041	PetM family of cytochrome b6f complex subunit 7 (PetM)	PetM family of cytochrome b6f complex subunit 7	-	Family
G, O	PF02529	Cytochrome B6-F complex subunit 5 (PetG)	Cytochrome B6-F complex subunit 5	-	Family
H, P	PF03742	PetN (PetN)	PetN	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, I	Cytochrome b6	electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II 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 photosynthesis	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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	electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity	transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport photosynthesis photosynthesis, light reaction transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport photosynthesis photosynthesis, light reaction photosynthetic electron transport chain cellular metabolic process electron transport chain metabolic process generation of precursor metabolites and energy	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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
C, K	Cytochrome f	binding organic cyclic compound 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 cellular metabolic process metabolic process cellular process	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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
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 electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter activity plastoquinol--plastocyanin reductase activity oxidoreduction-driven active transmembrane transporter activity 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 electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity oxidoreductase activity, acting on diphenols and related substances as donors primary active transmembrane transporter 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 cellular metabolic process metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore cellular anatomical entity thylakoid membrane intracellular organelle cell periphery plasma membrane-derived thylakoid membrane organelle intracellular non-membrane-bounded organelle plasma membrane region bacterial thylakoid intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane plasma membrane-derived chromatophore cellular anatomical entity thylakoid membrane intracellular organelle cell periphery plasma membrane-derived thylakoid membrane organelle intracellular non-membrane-bounded organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle intracellular membrane-bounded organelle
E, M	Cytochrome B6	-	-	membrane cellular anatomical entity
F, N	Cytochrome b6-f complex subunit 7	electron transfer activity	photosynthesis cellular metabolic process metabolic process cellular process	protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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	electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity	photosynthesis cellular metabolic process 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 cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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
H, P	Cytochrome b6-f complex subunit 8	electron transfer activity electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity	photosynthesis cellular metabolic process 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 cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle plasma membrane-derived chromatophore membrane membrane plasma membrane protein-containing complex intracellular anatomical structure cytochrome complex catalytic complex cellular anatomical entity intracellular organelle cytochrome b6f complex organelle intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle 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
A, I	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
A, I	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
A, I	IPR023530	Cytochrome b6, PetB	Family
A, I	IPR048259	Cytochrome b/b6, N-terminal domain, eukaryotic/bacterial	Domain
A, I	IPR005797	Cytochrome b/b6, N-terminal 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
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
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
F, N	IPR012595	PetM of cytochrome b6/f complex subunit 7	Family
G, O	IPR003683	Cytochrome b6/f complex, subunit 5	Family
G, O	IPR036099	Cytochrome b6/f complex, subunit 5 superfamily	Homologous Superfamily
H, P	IPR036143	Cytochrome b6-f complex, subunit 8 superfamily	Homologous Superfamily
H, P	IPR005497	Cytochrome b6-f complex, subunit 8	Family

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