7ZXY

3.15 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Synechocystis sp. PCC 6803 with natively bound plastoquinone and lipid molecules.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit.

Proctor, M.S.Malone, L.A.Farmer, D.A.Swainsbury, D.J.K.Hawkings, F.R.Pastorelli, F.Emrich-Mills, T.Z.Siebert, C.A.Hunter, C.N.Johnson, M.P.Hitchcock, A.

(2022) Biochem J 479: 1487-1503

  • DOI: https://doi.org/10.1042/BCJ20220124
  • Primary Citation of Related Structures:  
    7R0W, 7ZXY

  • PubMed Abstract: 

    In oxygenic photosynthesis, the cytochrome b6f (cytb6f) complex links the linear electron transfer (LET) reactions occurring at photosystems I and II and generates a transmembrane proton gradient via the Q-cycle. In addition to this central role in LET, cytb6f also participates in a range of processes including cyclic electron transfer (CET), state transitions and photosynthetic control. Many of the regulatory roles of cytb6f are facilitated by auxiliary proteins that differ depending upon the species, yet because of their weak and transient nature the structural details of these interactions remain unknown. An apparent key player in the regulatory balance between LET and CET in cyanobacteria is PetP, a ∼10 kDa protein that is also found in red algae but not in green algae and plants. Here, we used cryogenic electron microscopy to determine the structure of the Synechocystis sp. PCC 6803 cytb6f complex in the presence and absence of PetP. Our structures show that PetP interacts with the cytoplasmic side of cytb6f, displacing the C-terminus of the PetG subunit and shielding the C-terminus of cytochrome b6, which binds the heme cn cofactor that is suggested to mediate CET. The structures also highlight key differences in the mode of plastoquinone binding between cyanobacterial and plant cytb6f complexes, which we suggest may reflect the unique combination of photosynthetic and respiratory electron transfer in cyanobacterial thylakoid membranes. The structure of cytb6f from a model cyanobacterial species amenable to genetic engineering will enhance future site-directed mutagenesis studies of structure-function relationships in this crucial ET complex.


  • Organizational Affiliation

    Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6
A, I
222Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q57038 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q57038 
Go to UniProtKB:  Q57038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57038
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 4
B, J
160Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P27589 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P27589 
Go to UniProtKB:  P27589
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27589
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome f
C, K
284Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26287 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P26287 
Go to UniProtKB:  P26287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26287
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 2
D, L
180Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
Find proteins for P26290 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P26290 
Go to UniProtKB:  P26290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26290
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome B6
E, M
32Synechocystis sp. PCC 6803Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 7
F, N
36Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74810 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74810 
Go to UniProtKB:  P74810
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74810
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 5
G, O
37Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74149 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74149 
Go to UniProtKB:  P74149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74149
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 8
H, P
29Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P72717 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P72717 
Go to UniProtKB:  P72717
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72717
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
HA [auth J],
U [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PGV
Query on PGV

Download Ideal Coordinates CCD File 
DA [auth I]
IA [auth J]
JA [auth J]
KA [auth J]
V [auth B]
DA [auth I],
IA [auth J],
JA [auth J],
KA [auth J],
V [auth B],
W [auth B],
Z [auth C]
(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 I],
LA [auth K],
T [auth A],
X [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
EA [auth I],
FA [auth I],
R [auth A],
S [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ECH
Query on ECH

Download Ideal Coordinates CCD File 
CA [auth I],
Q [auth A]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
LFA
Query on LFA

Download Ideal Coordinates CCD File 
BA [auth E],
Y [auth C]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
AA [auth D],
MA [auth L]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011151/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V006630/1
Leverhulme TrustUnited KingdomRPG-2019-045

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references