7R0W

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein Cp097, conserved in cyanobacteriaA [auth X],
R [auth V]
65SynechocystisMutation(s): 0 
Gene Names: cp097D082_20950
UniProt
Find proteins for P72798 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP72798
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6B [auth I],
I [auth A]
222Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q57038 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupQ57038
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4C [auth J],
J [auth B]
160Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P27589 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP27589
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome fD [auth K],
K [auth C]
328Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26287 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP26287
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome B6E [auth M],
M [auth E]
32Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A6P1VG96 (Synechocystis sp. CACIAM 05)
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UniProt GroupA0A6P1VG96
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 7F [auth N],
N [auth F]
36Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74810 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP74810
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 5G [auth O],
O [auth G]
38Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74149 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 8H [auth P],
P [auth H]
29Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P72717 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske domain, PetCL [auth D],
Q [auth L]
192Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26290 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupP26290
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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IA [auth B],
Y [auth J]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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OA [auth D],
RA [auth L]
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

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BA [auth N]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
6PL
Query on 6PL

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CA [auth P],
QA [auth H]
(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

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FA [auth A],
X [auth J]
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

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KA [auth B],
LA [auth C],
V [auth I],
Z [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 (Subject of Investigation/LOI)
Query on HEC

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AA [auth K],
MA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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DA [auth A]
EA [auth A]
HA [auth B]
S [auth I]
T [auth I]
DA [auth A],
EA [auth A],
HA [auth B],
S [auth I],
T [auth I],
U [auth I]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
2WA
Query on 2WA

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JA [auth B](1S,8E)-1-{[(2S)-1-hydroxy-3-{[(1S)-1-hydroxypentadecyl]oxy}propan-2-yl]oxy}heptadec-8-en-1-ol
C35 H70 O5
YLBOKUFLARRKAJ-FAMWHJLKSA-N
ECH
Query on ECH

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GA [auth A],
W [auth I]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
LFA
Query on LFA

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PA [auth E]EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

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NA [auth D],
SA [auth L]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.20

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
Wellcome TrustUnited Kingdomnr21005

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