1Q90

Structure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 2.0 of the entry. See complete history


Literature

An Atypical Haem in the Cytochrome B6F Complex

Stroebel, D.Choquet, Y.Popot, J.-L.Picot, D.

(2003) Nature 426: 413-418

  • DOI: https://doi.org/10.1038/nature02155
  • Primary Citation of Related Structures:  
    1Q90

  • PubMed Abstract: 

    Photosystems I and II (PSI and II) are reaction centres that capture light energy in order to drive oxygenic photosynthesis; however, they can only do so by interacting with the multisubunit cytochrome b(6)f complex. This complex receives electrons from PSII and passes them to PSI, pumping protons across the membrane and powering the Q-cycle. Unlike the mitochondrial and bacterial homologue cytochrome bc(1), cytochrome b(6)f can switch to a cyclic mode of electron transfer around PSI using an unknown pathway. Here we present the X-ray structure at 3.1 A of cytochrome b(6)f from the alga Chlamydomonas reinhardtii. The structure bears similarities to cytochrome bc(1) but also exhibits some unique features, such as binding chlorophyll, beta-carotene and an unexpected haem sharing a quinone site. This haem is atypical as it is covalently bound by one thioether linkage and has no axial amino acid ligand. This haem may be the missing link in oxygenic photosynthesis.


  • Organizational Affiliation

    Laboratoire de Physico-Chimie Moléculaire des Membranes Biologiques, CNRS/Université Paris 7, UMR 7099, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apocytochrome f292Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETA
Membrane Entity: Yes 
UniProt
Find proteins for P23577 (Chlamydomonas reinhardtii)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6215Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETB
Membrane Entity: Yes 
UniProt
Find proteins for Q00471 (Chlamydomonas reinhardtii)
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UniProt GroupQ00471
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome B6-F complex iron-sulfur subunit127Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETC
EC: 1.10.99.1
Membrane Entity: Yes 
UniProt
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UniProt GroupP49728
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4159Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETD
Membrane Entity: Yes 
UniProt
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UniProt GroupP23230
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome B6-F complex iron-sulfur subunitE [auth R]49Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETC
EC: 1.10.99.1
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit petGF [auth G]37Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETG
Membrane Entity: Yes 
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UniProt GroupQ08362
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit petLG [auth L]32Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETL
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit PETMH [auth M]39Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETM
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit PETNI [auth N]31Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETN
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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Q [auth D]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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T [auth R]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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S [auth D],
U [auth L]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
HEC
Query on HEC

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J [auth A],
K [auth B],
L [auth B],
M [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
BCR
Query on BCR

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N [auth B]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
TDS
Query on TDS

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R [auth D]8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
LFA
Query on LFA

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O [auth B]EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
FES
Query on FES

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P [auth C]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.454α = 90
b = 171.205β = 90
c = 351.009γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary