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: 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 ...

    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. matt.johnson@sheffield.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6I [auth A], A [auth I]215Spinacia oleraceaMutation(s): 0 
Gene Names: petB
Membrane Entity: Yes 
UniProt
Find proteins for P00165 (Spinacia oleracea)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4J [auth B], B [auth J]160Spinacia oleraceaMutation(s): 0 
Gene Names: petD
Membrane Entity: Yes 
UniProt
Find proteins for P00166 (Spinacia oleracea)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome fK [auth C], C [auth K]285Spinacia oleraceaMutation(s): 0 
Gene Names: petA
Membrane Entity: Yes 
UniProt
Find proteins for P16013 (Spinacia oleracea)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunit, chloroplasticL [auth D], D [auth L]179Spinacia oleraceaMutation(s): 0 
Gene Names: petC
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
Find proteins for P08980 (Spinacia oleracea)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 6M [auth E], E [auth M]31Spinacia oleraceaMutation(s): 0 
Gene Names: petL
Membrane Entity: Yes 
UniProt
Find proteins for Q9M3L0 (Spinacia oleracea)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7N [auth F], F [auth N]36Spinacia oleraceaMutation(s): 0 
Gene Names: petM
Membrane Entity: Yes 
UniProt
Find proteins for P80883 (Spinacia oleracea)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5O [auth G], G [auth O]37Spinacia oleraceaMutation(s): 0 
Gene Names: petGpetE
Membrane Entity: Yes 
UniProt
Find proteins for P69461 (Spinacia oleracea)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8P [auth H], H [auth P]29Spinacia oleraceaMutation(s): 0 
Gene Names: petNycf6
Membrane Entity: Yes 
UniProt
Find proteins for P61045 (Spinacia oleracea)
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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HA [auth A], T [auth I]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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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
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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RA [auth F], X [auth J]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
6PL (Subject of Investigation/LOI)
Query on 6PL

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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
 Ligand Interaction
PL9 (Subject of Investigation/LOI)
Query on PL9

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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
 Ligand Interaction
PGV (Subject of Investigation/LOI)
Query on PGV

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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
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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GA [auth A], NA [auth C], S [auth I], Z [auth K]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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EA [auth A], FA [auth A], Q [auth I], R [auth I]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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SA [auth H], U [auth I]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
FES
Query on FES

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BA [auth L], PA [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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