6rqf

3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules

Method: ELECTRON MICROSCOPY

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b6

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYB6_SPIOL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 1–215 Author chain I； PDBConstruct 1–215； UniProt 1–215

Cytochrome b6-f complex subunit 4

OrganismNot specified

UniProt P00166

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PETD_SPIOL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–160； UniProt 1–160 Author chain J； PDBConstruct 1–160； UniProt 1–160

Cytochrome f

OrganismNot specified

UniProt P16013

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYF_SPIOL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–285； UniProt 36–320 Author chain K； PDBConstruct 1–285； UniProt 36–320

Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

OrganismNot specified

UniProt P08980

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UCRIA_SPIOL
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–179； UniProt 52–230 Author chain L； PDBConstruct 1–179； UniProt 52–230

Cytochrome b6-f complex subunit 6

OrganismNot specified

UniProt Q9M3L0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PETL_SPIOL
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–31； UniProt 1–31 Author chain M； PDBConstruct 1–31； UniProt 1–31

Cytochrome b6-f complex subunit 7

OrganismNot specified

UniProt P80883

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 5 × 2 （P69461） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PETM_SPIOL
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–36； UniProt 1–36 Author chain N； PDBConstruct 1–36； UniProt 1–36

Cytochrome b6-f complex subunit 5

OrganismNot specified

UniProt P69461

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 8 × 2 （P61045） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PETG_SPIOL
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–37； UniProt 1–37 Author chain O； PDBConstruct 1–37； UniProt 1–37

Cytochrome b6-f complex subunit 8

OrganismNot specified

UniProt P61045

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Cytochrome b6 × 2 （P00165） Cytochrome b6-f complex subunit 4 × 2 （P00166） Cytochrome f × 2 （P16013） Cytochrome b6-f complex iron-sulfur subunit, chloroplastic × 2 （P08980） Cytochrome b6-f complex subunit 6 × 2 （Q9M3L0） Cytochrome b6-f complex subunit 7 × 2 （P80883） Cytochrome b6-f complex subunit 5 × 2 （P69461） PROTOPORPHYRIN IX CONTAINING FE × 4 HEME C × 4 CHLOROPHYLL A × 2 BETA-CAROTENE × 2 ;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ; × 3 (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 3 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE × 2 (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 FE2/S2 (INORGANIC) CLUSTER × 2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PETN_SPIOL
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–29； UniProt 1–29 Author chain P； PDBConstruct 1–29； UniProt 1–29

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6rqf
Deposition date deposition_date	2019-05-15
Structure title title	3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules
Keywords keywords	Plastoquinol-plastocyanin oxido-reductase Cytochrome b6f Photosynthesis Electron transport, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6rqf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6rqf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6rqf__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.40 Å
Rg (electron density)	41.92 Å
Total Rg	42.36 Å
Atom count	16359
Residues	1944
Excluded volume	301980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6rqf__assembly_1__model_1`	hexadecameric （16）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	Cytochrome b6
Molecular weight formula_weight	24186.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,A
Atom count atom_count	16359

MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRPTVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVTGVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTLTRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL

Entity 2 Entity 2 polymer

Description description	Cytochrome b6-f complex subunit 4
Molecular weight formula_weight	17456.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,B

MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPSMIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKFQNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF

Entity 3 Entity 3 polymer

Description description	Cytochrome f
Molecular weight formula_weight	31357.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,C

YPIFAQQGYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAPPDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSEITFPILAPDPATKKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVDIIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQIFLVLKKKQFEKVQLSEMNF

Entity 4 Entity 4 polymer

Description description	Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
Molecular weight formula_weight	18956.5 kDa
EC 编号 ec_number	7.1.1.6
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,D

ATSIPADNVPDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA

Entity 5 Entity 5 polymer

Description description	Cytochrome b6-f complex subunit 6
Molecular weight formula_weight	3452.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,E

MFTLTSYFGFLLAALTITSALFIGLNKIRLI

Entity 6 Entity 6 polymer

Description description	Cytochrome b6-f complex subunit 7
Molecular weight formula_weight	3774.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,F

NAAAEIFRIAAVMNGLTLVGVAIGFVLLRIEATVEE

Entity 7 Entity 7 polymer

Description description	Cytochrome b6-f complex subunit 5
Molecular weight formula_weight	4172.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,G

MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL

Entity 8 Entity 8 polymer

Description description	Cytochrome b6-f complex subunit 8
Molecular weight formula_weight	3170.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,H

MDIVSLAWAALMVVFTFSLSLVVWGRSGL

Entity 9 Entity 9 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	CHLOROPHYLL A
Molecular weight formula_weight	893.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	BETA-CAROTENE
Molecular weight formula_weight	536.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 13 Entity 13 non-polymer

Description description	;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ;
Molecular weight formula_weight	749.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 14 Entity 14 non-polymer

Description description	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
Molecular weight formula_weight	763.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 15 Entity 15 non-polymer

Description description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Molecular weight formula_weight	787.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 16 Entity 16 non-polymer

Description description	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
Molecular weight formula_weight	749.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 17 Entity 17 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 18 Entity 18 non-polymer

Description description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Molecular weight formula_weight	795.1 kDa
Source method src_method	syn
Copy count entity_count	3

▼

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	6rqfA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

Domain ID domain_id	6rqfB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	510 — Single helix bin

Domain ID domain_id	6rqfB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	980 — plastocyanin oxidoreductase

Domain ID domain_id	6rqfC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	830 — Cytochrome f large domain

Domain ID domain_id	6rqfC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

Domain ID domain_id	6rqfI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	810 — Cytochrome Bc1 Complex; Chain C
Homologous superfamily homologous superfamily	10 — Cytochrome Bc1 Complex; Chain C

Domain ID domain_id	6rqfJ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	510 — Single helix bin

Domain ID domain_id	6rqfJ02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	980 — plastocyanin oxidoreductase

Domain ID domain_id	6rqfK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	830 — Cytochrome f large domain

Domain ID domain_id	6rqfK02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.58 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	108560

3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome f

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex iron-sulfur subunit, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex subunit 6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex subunit 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome b6-f complex subunit 8

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6rqf__assembly_1__model_1

6rqf__assembly_1__model_1 | I(q)

6rqf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer