1VF5

Crystal Structure of Cytochrome b6f Complex from M.laminosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

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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: https://doi.org/10.1126/science.1090165
  • Primary Citation of Related Structures:  
    1VF5

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B6A,
I [auth N]
215Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83791
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SUBUNIT IVB,
J [auth O]
160Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P83792 (Mastigocladus laminosus)
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UniProt GroupP83792
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME FC,
K [auth P]
289Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83793
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIESKE IRON-SULFUR PROTEIND,
L [auth Q]
179Mastigocladus laminosusMutation(s): 0 
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
Find proteins for P83794 (Mastigocladus laminosus)
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UniProt GroupP83794
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PET LE,
M [auth R]
32Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83795
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PET MF,
N [auth S]
35Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83796
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PET GG,
O [auth T]
37Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83797
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN PET NH,
P [auth U]
29Mastigocladus laminosusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP83798
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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GA [auth O],
W [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
OPC
Query on OPC

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FA [auth N],
JA [auth Q],
V [auth B],
Y [auth D]
(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
C45 H87 N O8 P
CTQFGTDUPDRLRZ-CNMUNUSJSA-O
PL9
Query on PL9

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IA [auth Q],
U [auth A]
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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
HEM
Query on HEM

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BA [auth N]
CA [auth N]
DA [auth N]
HA [auth P]
Q [auth A]
BA [auth N],
CA [auth N],
DA [auth N],
HA [auth P],
Q [auth A],
R [auth A],
S [auth A],
X [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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AA [auth E],
LA [auth R]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
TDS
Query on TDS

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EA [auth N],
T [auth A]
8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE
C25 H38 O5
LSHATXKKRQGSEC-UHFFFAOYSA-N
FES
Query on FES

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KA [auth Q],
Z [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.536α = 90
b = 157.536β = 90
c = 360.347γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary