1VF5

Crystal Structure of Cytochrome b6f Complex from M.laminosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Cytochrome B6F Complex of Oxygenic Photosynthesis: Tuning the Cavity

Kurisu, G.Zhang, H.Smith, J.L.Cramer, W.A.

(2003) Science 302: 1009-1014

  • DOI: 10.1126/science.1090165

  • PubMed Abstract: 
  • The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. ...

    The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.


    Related Citations: 
    • A Defined Protein-Detergent-Lipid Complex for Crystallization of Integral Membrane Proteins: The Cytochrome B6F Complex of Oxygenic Photosynthesis
      Zhang, H.,Kurisu, G.,Smith, J.L.,Cramer, W.A.
      (2003) Proc.Natl.Acad.Sci.USA 100: 5160


    Organizational Affiliation

    Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B6
A, N
215Mastigocladus laminosusGene Names: petB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83791 (Mastigocladus laminosus)
Go to UniProtKB:  P83791
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUBUNIT IV
B, O
160Mastigocladus laminosusGene Names: petD
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83792 (Mastigocladus laminosus)
Go to UniProtKB:  P83792
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME F
C, P
289Mastigocladus laminosusGene Names: petA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83793 (Mastigocladus laminosus)
Go to UniProtKB:  P83793
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIESKE IRON-SULFUR PROTEIN
D, Q
179Mastigocladus laminosusGene Names: petC
EC: 1.10.9.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83794 (Mastigocladus laminosus)
Go to UniProtKB:  P83794
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PET L
E, R
32Mastigocladus laminosusGene Names: petL
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83795 (Mastigocladus laminosus)
Go to UniProtKB:  P83795
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PET M
F, S
35Mastigocladus laminosusGene Names: petM
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83796 (Mastigocladus laminosus)
Go to UniProtKB:  P83796
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PET G
G, T
37Mastigocladus laminosusGene Names: petG
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83797 (Mastigocladus laminosus)
Go to UniProtKB:  P83797
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PROTEIN PET N
H, U
29Mastigocladus laminosusGene Names: petN
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Cytochrome b6f of Oxygenic Photosynthesis
Protein: 
Cytochrome b6f complex
Find proteins for P83798 (Mastigocladus laminosus)
Go to UniProtKB:  P83798
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download SDF File 
Download CCD File 
B, O
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PL9
Query on PL9

Download SDF File 
Download CCD File 
A, Q
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
PLASTOQUINONE 9
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
OPC
Query on OPC

Download SDF File 
Download CCD File 
B, D, N, Q
(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
DIOLEOYL-PHOSPHATIDYLCHOLINE
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
D, Q
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
TDS
Query on TDS

Download SDF File 
Download CCD File 
A, N
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, C, N, P
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 
E, R
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.258 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 157.536α = 90.00
b = 157.536β = 90.00
c = 360.347γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance