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 6RQF | pdb_00006rqf

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6RQF

This is version 3.0 of the entry. See complete history. 

Literature

Cryo-EM structure of the spinach cytochrome b6f complex at 3.6 angstrom resolution.

Malone, L.A., Qian, P., Mayneord, G.E., Hitchcock, A., Farmer, D.A., Thompson, R.F., Swainsbury, D.J.K., Ranson, N.A., Hunter, C.N., Johnson, M.P.

(2019) Nature 575: 535-539

  • DOI: https://doi.org/10.1038/s41586-019-1746-6
  • Primary Citation Related Structures: 
    6RQF

  • PubMed Abstract: 

    The cytochrome b 6  f (cytb 6  f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane proton gradient for ATP synthesis 1-3 . Electron transfer within cytb 6  f occurs via the quinol (Q) cycle, which catalyses the oxidation of plastoquinol (PQH 2 ) and the reduction of both plastocyanin (PC) and plastoquinone (PQ) at two separate sites via electron bifurcation 2 . In higher plants, cytb 6  f also acts as a redox-sensing hub, pivotal to the regulation of light harvesting and cyclic electron transfer that protect against metabolic and environmental stresses 3 . Here we present a 3.6 Å resolution cryo-electron microscopy (cryo-EM) structure of the dimeric cytb 6  f complex from spinach, which reveals the structural basis for operation of the Q cycle and its redox-sensing function. The complex contains up to three natively bound PQ molecules. The first, PQ1, is located in one cytb 6  f monomer near the PQ oxidation site (Q p ) adjacent to haem b p and chlorophyll a. Two conformations of the chlorophyll a phytyl tail were resolved, one that prevents access to the Q p site and another that permits it, supporting a gating function for the chlorophyll a involved in redox sensing. PQ2 straddles the intermonomer cavity, partially obstructing the PQ reduction site (Q n ) on the PQ1 side and committing the electron transfer network to turnover at the occupied Q n site in the neighbouring monomer. A conformational switch involving the haem c n propionate promotes two-electron, two-proton reduction at the Q n site and avoids formation of the reactive intermediate semiquinone. The location of a tentatively assigned third PQ molecule is consistent with a transition between the Q p and Q n sites in opposite monomers during the Q cycle. The spinach cytb 6  f structure therefore provides new insights into how the complex fulfils its catalytic and regulatory roles in photosynthesis.


  • Organizational Affiliation: 
    • Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.

Macromolecule Content 

  • Total Structure Weight: 232.71 kDa 
  • Atom Count: 16,359 
  • Modeled Residue Count: 1,944 
  • Deposited Residue Count: 1,944 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6A [auth I],
I [auth A]
215Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00165 (Spinacia oleracea)
Explore P00165 
Go to UniProtKB:  P00165
Entity Groups
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UniProt GroupP00165
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4B [auth J],
J [auth B]
160Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00166 (Spinacia oleracea)
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UniProt GroupP00166
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome fC [auth K],
K [auth C]
285Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16013 (Spinacia oleracea)
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UniProt GroupP16013
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit, chloroplasticD [auth L],
L [auth D]
179Spinacia oleraceaMutation(s): 0 
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
Find proteins for P08980 (Spinacia oleracea)
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UniProt GroupP08980
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6E [auth M],
M [auth E]
31Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9M3L0 (Spinacia oleracea)
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UniProt GroupQ9M3L0
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7F [auth N],
N [auth F]
36Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P80883 (Spinacia oleracea)
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UniProt GroupP80883
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5G [auth O],
O [auth G]
37Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P69461 (Spinacia oleracea)
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UniProt GroupP69461
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8H [auth P],
P [auth H]
29Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61045 (Spinacia oleracea)
Explore P61045 
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA



Download:Ideal Coordinates CCD File
HA [auth A],
T [auth I]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD

Query on SQD



Download:Ideal Coordinates CCD File
CA [auth L],
KA [auth A],
OA [auth C]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG



Download:Ideal Coordinates CCD File
RA [auth F],
X [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
6PL

Query on 6PL



Download:Ideal Coordinates CCD File
DA [auth N],
QA [auth E],
W [auth I]
(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-RRHRGVEJSA-O
PL9

Query on PL9



Download:Ideal Coordinates CCD File
IA [auth A],
JA [auth A],
V [auth I]
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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
AA [auth K],
LA [auth A],
MA [auth B],
Y [auth J]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
GA [auth A],
NA [auth C],
S [auth I],
Z [auth K]
HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM



Download:Ideal Coordinates CCD File
EA [auth A],
FA [auth A],
Q [auth I],
R [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
SA [auth H],
U [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
BA [auth L],
PA [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M000265/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P002005/1
Leverhulme TrustUnited KingdomRPG-2016-161

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Derived calculations
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Database references
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Non-polymer description, Structure summary
  • Version 2.1: 2025-07-02
    Changes: Data collection, Structure summary
  • Version 2.2: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2026-09-02
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary