6RQF

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


This is version 1.3 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00165
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P00166 
Go to UniProtKB:  P00166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00166
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P16013 
Go to UniProtKB:  P16013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16013
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P08980 
Go to UniProtKB:  P08980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08980
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore Q9M3L0 
Go to UniProtKB:  Q9M3L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M3L0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P80883 
Go to UniProtKB:  P80883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80883
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P69461 
Go to UniProtKB:  P69461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69461
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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 
Go to UniProtKB:  P61045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61045
Sequence Annotations
Expand
  • 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 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
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
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