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 

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
  • 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 ...

    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 U S A 100: 5160

    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
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME B6A, I [auth N]215Mastigocladus laminosusMutation(s): 0 
Gene Names: petB
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUBUNIT IVB, J [auth O]160Mastigocladus laminosusMutation(s): 0 
Gene Names: petD
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME FC, K [auth P]289Mastigocladus laminosusMutation(s): 0 
Gene Names: petA
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RIESKE IRON-SULFUR PROTEIND, L [auth Q]179Mastigocladus laminosusMutation(s): 0 
Gene Names: petC
EC: 7.1.1.6
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN PET LE, M [auth R]32Mastigocladus laminosusMutation(s): 0 
Gene Names: petL
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN PET MF, N [auth S]35Mastigocladus laminosusMutation(s): 0 
Gene Names: petM
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN PET GG, O [auth T]37Mastigocladus laminosusMutation(s): 0 
Gene Names: petG
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN PET NH, P [auth U]29Mastigocladus laminosusMutation(s): 0 
Gene Names: petN
Membrane Entity: Yes 
UniProt
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
HEM
Query on HEM

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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
 Ligand Interaction
BCR
Query on BCR

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

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KA [auth Q], Z [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
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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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