7ZYV | pdb_00007zyv

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A 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: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	Transmembrane di-heme cytochromes	8094397	3000517	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transmembrane di-heme cytochromes	8094397	3000517	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	8093928	3000966	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	8093928	3000966	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ISP domain	8041548	3000233	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ISP domain	8041548	3000233	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	PetN subunit of the cytochrome b6f complex	8094653	3000279	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PetN subunit of the cytochrome b6f complex	8094653	3000279	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)
I		e7zyvI1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
A		e7zyvA1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
J		e7zyvJ1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
B		e7zyvB1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
L		e7zyvL2	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
D		e7zyvD1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
M		e7zyvM1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
E		e7zyvE1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
N		e7zyvN1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
F		e7zyvF1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
O		e7zyvO1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
G		e7zyvG1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
P		e7zyvP1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
H		e7zyvH1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (develop294)
Q [auth R]	WD40, ANAPC4_WD40, WD40_CDC20-Fz	e7zyvR01	A: alpha bundles	X: Rossmann-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: WD40, ANAPC4_WD40, WD40_CDC20-Fz	ECOD (develop294)

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
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
E, M	PF05115	Cytochrome B6-F complex subunit VI (PetL) (PetL)	Cytochrome B6-F complex subunit VI (PetL)	-	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	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	cellular anatomical structure membrane chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope bounding membrane of organelle membraneless organelle cellular anatomical structure membrane chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle 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	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane
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	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane
D, L	Cytochrome b6-f complex iron-sulfur subunit, chloroplastic	oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 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 oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding 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 photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane cell periphery plasma membrane
E, M	Cytochrome b6-f complex subunit 6	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 chloroplast thylakoid membrane membrane-bounded organelle plastid 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast membrane intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane
F, N	Cytochrome b6-f complex subunit 7	-	-	-
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 chloroplast thylakoid membrane membrane-bounded organelle plastid 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast membrane intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane
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 chloroplast thylakoid membrane membrane-bounded organelle plastid 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast membrane intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane
Q [auth R], R [auth Q]	Thylakoid soluble phosphoprotein	protein-containing complex binding binding chloroplast photosystem I binding lipid binding chloroplast photosystem II binding PSII associated light-harvesting complex II binding	response to light stimulus response to stimulus response to radiation response to abiotic stimulus	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membrane membraneless organelle intracellular membraneless organelle photosynthetic membrane thylakoid membrane thylakoid membrane-bounded organelle plastid cytoplasm intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membrane membraneless organelle intracellular membraneless organelle photosynthetic membrane thylakoid membrane thylakoid membrane-bounded organelle plastid cytoplasm intracellular membrane-bounded organelle chloroplast

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	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
E, M	IPR007802	Cytochrome b6-f complex subunit 6	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
Q [auth R], R [auth Q]	IPR037244	Thylakoid soluble phosphoprotein TSP9 superfamily	Homologous Superfamily
Q [auth R], R [auth Q]	IPR021584	Thylakoid soluble phosphoprotein TSP9	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, G, H, I, J, K, L, M, 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, G, H, I, J, K, L, M, 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, G, H, I, J, K, L, M, O, P	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Cytochrome b₆f of Oxygenic Photosynthesis	dimeric cytochrome b₆f complex with bound plastoquinones