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


Ligand Structure Quality Assessment 


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: 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apocytochrome fA292Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petA
Membrane Entity: Yes 
UniProt
Find proteins for P23577 (Chlamydomonas reinhardtii)
Explore P23577 
Go to UniProtKB:  P23577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23577
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6B215Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petB
Membrane Entity: Yes 
UniProt
Find proteins for Q00471 (Chlamydomonas reinhardtii)
Explore Q00471 
Go to UniProtKB:  Q00471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00471
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
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)
Membrane Entity: Yes 
UniProt
Find proteins for P49728 (Chlamydomonas reinhardtii)
Explore P49728 
Go to UniProtKB:  P49728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49728
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4D159Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petD
Membrane Entity: Yes 
UniProt
Find proteins for P23230 (Chlamydomonas reinhardtii)
Explore P23230 
Go to UniProtKB:  P23230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23230
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome B6-F complex iron-sulfur subunitE [auth R]49Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petC
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P49728 (Chlamydomonas reinhardtii)
Explore P49728 
Go to UniProtKB:  P49728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49728
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit petGF [auth G]37Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petG
Membrane Entity: Yes 
UniProt
Find proteins for Q08362 (Chlamydomonas reinhardtii)
Explore Q08362 
Go to UniProtKB:  Q08362
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08362
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit petLG [auth L]32Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petL
Membrane Entity: Yes 
UniProt
Find proteins for P50369 (Chlamydomonas reinhardtii)
Explore P50369 
Go to UniProtKB:  P50369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50369
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit PETMH [auth M]39Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: petM, petX
Membrane Entity: Yes 
UniProt
Find proteins for Q42496 (Chlamydomonas reinhardtii)
Explore Q42496 
Go to UniProtKB:  Q42496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ42496
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6f complex subunit PETNI [auth N]31Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PETN, CHLREDRAFT_177155
Membrane Entity: Yes 
UniProt
Find proteins for P0C1D4 (Chlamydomonas reinhardtii)
Explore P0C1D4 
Go to UniProtKB:  P0C1D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1D4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
Download Ideal Coordinates CCD File 
Q [auth D]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M		 Ligand Interaction
SQD
Query on SQD
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
LMG
Query on LMG
Download Ideal Coordinates CCD File 
S [auth D],
U [auth L]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N		 Ligand Interaction
HEC
Query on HEC
Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
L [auth B],
M [auth B]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
BCR
Query on BCR
Download Ideal Coordinates CCD File 
N [auth B]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N		 Ligand Interaction
TDS
Query on TDS
Download Ideal Coordinates CCD File 
R [auth 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
Download Ideal Coordinates CCD File 
O [auth B]EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
P [auth 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

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

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