1Q90

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nature02155

  • 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 f ...

    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.

    Related Citations: 
    • Chimeric Fusions of Subunits IV and PET L in the Cytochrome B6F complex of chlamydomonas reinhardtii: structural implications and consequences on state transitions
      Zito, F.,Vinh, J.,Popot, J.L.,Finazzi, G.
      (2002) J.Biol.Chem. 277: 12446

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome f
A
292Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petA
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P23577 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P23577
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6
B
215Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petB
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for Q00471 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q00471
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome B6-F complex iron-sulfur subunit
C
127Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petC
EC: 7.1.1.6
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P49728 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P49728
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 4
D
159Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petD
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P23230 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P23230
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome B6-F complex iron-sulfur subunit
R
49Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petC
EC: 7.1.1.6
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P49728 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P49728
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit petG
G
37Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petG
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for Q08362 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q08362
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit petL
L
32Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petL
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P50369 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P50369
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit PETM
M
39Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petM (petX)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for Q42496 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q42496
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit PETN
N
31Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETN
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis		Protein: 
Cytochrome b6f complex
Find proteins for P0C1D4 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P0C1D4
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD
Download SDF File 
Download CCD File 
R
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
CLA
Query on CLA
Download SDF File 
Download CCD File 
D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG
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Download CCD File 
D, L
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
FES
Query on FES
Download SDF File 
Download CCD File 
C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TDS
Query on TDS
Download SDF File 
Download CCD File 
D
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
TRIDECYL-STIGMATELLIN
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR
Download SDF File 
Download CCD File 
B
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LFA
Query on LFA
Download SDF File 
Download CCD File 
B
EICOSANE
LIPID FRAGMENT
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.454α = 90.00
b = 171.205β = 90.00
c = 351.009γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
MLPHAREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-07-25
    Type: Non-polymer description