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 

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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apocytochrome fA292Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petA
Find proteins for P23577 (Chlamydomonas reinhardtii)
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6B215Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petB
Find proteins for Q00471 (Chlamydomonas reinhardtii)
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome B6-F complex iron-sulfur subunitC127Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petC
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Find proteins for P49728 (Chlamydomonas reinhardtii)
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6-f complex subunit 4D159Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petD
Find proteins for P23230 (Chlamydomonas reinhardtii)
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome B6-F complex iron-sulfur subunitR49Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petC
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Find proteins for P49728 (Chlamydomonas reinhardtii)
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit petGG37Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petG
Find proteins for Q08362 (Chlamydomonas reinhardtii)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit petLL32Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petL
Find proteins for P50369 (Chlamydomonas reinhardtii)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit PETMM39Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petM, petX
Find proteins for Q42496 (Chlamydomonas reinhardtii)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6f complex subunit PETNN31Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETN, CHLREDRAFT_177155
Find proteins for P0C1D4 (Chlamydomonas reinhardtii)
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
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D
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M		 Ligand Interaction
SQD
Query on SQD
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R
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
Query on LMG
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D, L
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
HEM
Query on HEM
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A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
BCR
Query on BCR
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B
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
TDS
Query on TDS
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D
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N		 Ligand Interaction
LFA
Query on LFA
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B
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
FES
Query on FES
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C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
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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Entry History 

Deposition Data

Revision History 

  • 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