2ZT9 | pdb_00002zt9

Crystal Structure of the Cytochrome b6f Complex from Nostoc sp. PCC 7120

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d2zt9h_	Membrane and cell surface proteins and peptides	Single transmembrane helix	PetN subunit of the cytochrome b6f complex	PetN subunit of the cytochrome b6f complex	automated matches	(Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
F	d2zt9f_	Membrane and cell surface proteins and peptides	Single transmembrane helix	PetM subunit of the cytochrome b6f complex	PetM subunit of the cytochrome b6f complex	automated matches	(Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
B	d2zt9b_	Membrane and cell surface proteins and peptides	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	automated matches	(Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)
A	d2zt9a_	Membrane and cell surface proteins and peptides	Heme-binding four-helical bundle	Transmembrane di-heme cytochromes	Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	automated matches	(Nostoc sp. PCC 7120 = FACHB-418 ) [TaxId: 103690 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2 Family	PetN subunit of the cytochrome b6f complex	8076380	4001705	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	PetN subunit of the cytochrome b6f complex	8076381	3000279	SCOP2 (2022-06-29)
F	SCOP2 Family	PetM subunit of the cytochrome b6f complex	8083553	4001695	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	PetM subunit of the cytochrome b6f complex	8083554	3000262	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	cytochrome f, large domain	8032340	3000800	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	cytochrome f, large domain	8032340	3000800	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Rudiment single hybrid motif	8032341	3001910	SCOP2B (2022-06-29)
B	SCOP2 Family	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	8078664	4002216	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	8078665	3000966	SCOP2 (2022-06-29)
A	SCOP2 Family	Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	8083549	4002208	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Transmembrane di-heme cytochromes	8083550	3000517	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)
H	PetN	e2zt9H1	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: PetN	ECOD (1.6)
G	PetG	e2zt9G1	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: PetG	ECOD (1.6)
F	PetM	e2zt9F1	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: PetM	ECOD (1.6)
E	PetL_1	e2zt9E1	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: PetL_1	ECOD (1.6)
D	Rieske_cytochrome_b6f	e2zt9D1	A: beta sandwiches	X: ISP domain (From Topology)	H: ISP domain (From Topology)	T: ISP domain	F: Rieske_cytochrome_b6f	ECOD (1.6)
D	Rieske_4	e2zt9D3	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Rieske_4	ECOD (1.6)
D	CytB6-F_Fe-S	e2zt9D2	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: CytB6-F_Fe-S	ECOD (1.6)
C	Apocytochr_F_N	e2zt9C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Apocytochr_F_N	ECOD (1.6)
C	Apocytochr_F_C_N	e2zt9C3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Apocytochr_F_C_N	ECOD (1.6)
C	Apocytochr_F_C_C	e2zt9C2	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: Apocytochr_F_C_C	ECOD (1.6)
B	Cytochrom_B_C	e2zt9B1	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	e2zt9A1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.5.700	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
D	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
C	2.60.40.830	Mainly Beta	Sandwich	Immunoglobulin-like	Cytochrome f large domain	CATH (4.3.0)
C	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
C	1.20.5.700	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
B	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)
B	1.10.287.980	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	plastocyanin oxidoreductase	CATH (4.3.0)
A	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H	PF03742	PetN (PetN)	PetN	-	Family
G	PF02529	Cytochrome B6-F complex subunit 5 (PetG)	Cytochrome B6-F complex subunit 5	-	Family
F	PF08041	PetM family of cytochrome b6f complex subunit 7 (PetM)	PetM family of cytochrome b6f complex subunit 7	-	Family
E	PF05115	Cytochrome B6-F complex subunit VI (PetL) (PetL)	Cytochrome B6-F complex subunit VI (PetL)	-	Family
D	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	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	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	PF00032	Cytochrome b(C-terminal)/b6/petD (Cytochrom_B_C)	Cytochrome b(C-terminal)/b6/petD		Domain
A	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	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	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	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	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 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
D	Cytochrome b6-f complex iron-sulfur subunit 1	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monooxygenase activity oxidoreductase activity catalytic 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 iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding monooxygenase activity oxidoreductase activity catalytic 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	Apocytochrome 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	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
B	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	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
A	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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H	IPR036143	Cytochrome b6-f complex, subunit 8 superfamily	Homologous Superfamily
H	IPR005497	Cytochrome b6-f complex, subunit 8	Family
G	IPR003683	Cytochrome b6/f complex, subunit 5	Family
G	IPR036099	Cytochrome b6/f complex, subunit 5 superfamily	Homologous Superfamily
F	IPR012595	PetM of cytochrome b6/f complex subunit 7	Family
E	IPR007802	Cytochrome b6-f complex subunit 6	Family
D	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
D	IPR014349	Rieske iron-sulphur protein	Family
D	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
D	IPR005805	Rieske iron-sulphur protein, C-terminal	Domain
D	IPR023960	Cytochrome b6-f complex iron-sulfur subunit	Family
D	IPR057415	Cytochrome b6-f complex iron-sulfur subunit-like, transmembrane anchor	Domain
C	IPR002325	Cytochrome f	Family
C	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
C	IPR036826	Cytochrome f large domain superfamily	Homologous Superfamily
C	IPR024058	Cytochrome f transmembrane anchor	Homologous Superfamily
C	IPR024094	Cytochrome f large domain	Domain
B	IPR036150	Cytochrome b/b6, C-terminal domain superfamily	Homologous Superfamily
B	IPR005798	Cytochrome b/b6, C-terminal	Domain
B	IPR005870	Cytochrome b6/f complex, subunit IV	Family
B	IPR048260	Cytochrome b/b6, C-terminal domain, eukaryotic/bacterial	Domain
A	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
A	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
A	IPR023530	Cytochrome b6, PetB	Family
A	IPR048259	Cytochrome b/b6, N-terminal domain, eukaryotic/bacterial	Domain
A	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, G, H	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	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, G, H	MemProtMD	Annotated as membrane protein by MemProtMD

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	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Cytochrome b₆f of Oxygenic Photosynthesis	Cytochrome b₆f complex