2D2C

Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex

Yan, J.Kurisu, G.Cramer, W.A.

(2006) Proc Natl Acad Sci U S A 103: 69-74

  • DOI: 10.1073/pnas.0504909102
  • Primary Citation of Related Structures:  
    2D2C

  • PubMed Abstract: 
  • Details are presented of the structural analysis of the cytochrome b(6)f complex from the thermophilic cyanobacterium, Mastigocladus laminosus, in the presence of the electrochemically positive (p)-side quinone analogue inhibitor, 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB) ...

    Details are presented of the structural analysis of the cytochrome b(6)f complex from the thermophilic cyanobacterium, Mastigocladus laminosus, in the presence of the electrochemically positive (p)-side quinone analogue inhibitor, 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB). One DBMIB binding site was found. This site is peripheral to the quinone binding space defined by the binding sites of other p-side inhibitors previously resolved in cytochrome bc(1)/b(6)f complexes. This high-affinity site resides in a p-side interfacial niche bounded by cytochrome f, subunit IV, and cytochrome b(6), is close (8 A) to the p-side heme b, but distant (19 A) from the [2Fe-2S] cluster. No significant electron density associated with the DBMIB was found elsewhere in the structure. However, the site at which DBMIB can inhibit light-induced redox turnover is within a few A of the [2Fe-2S] cluster, as shown by the absence of inhibition in mutants of Synechococcus sp. PCC 7002 at iron sulfur protein-Leu-111 near the cluster. The ability of a minimum amount of initially oxidized DBMIB to inhibit turnover of WT complex after a second light flash implies that there is a light-activated movement of DBMIB from the distal peripheral site to an inhibitory site proximal to the [2Fe-2S] cluster. Together with the necessary passage of quinone/quinol through the small Q(p) portal in the complex, it is seen that transmembrane traffic of quinone-like molecules through the core of cytochrome bc complexes can be labyrinthine.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, 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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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit 4B, J [auth O]160Mastigocladus laminosusMutation(s): 0 
Gene Names: petD
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Apocytochrome fC, K [auth P]289Mastigocladus laminosusMutation(s): 0 
Gene Names: petA
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex iron-sulfur subunitD, L [auth Q]179Mastigocladus laminosusMutation(s): 0 
Gene Names: petC
EC: 1.10.99.1 (PDB Primary Data), 7.1.1.6 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit VIE, M [auth R]32Mastigocladus laminosusMutation(s): 0 
Gene Names: petL
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit VIIF, N [auth S]35Mastigocladus laminosusMutation(s): 0 
Gene Names: petM
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit VG, O [auth T]37Mastigocladus laminosusMutation(s): 0 
Gene Names: petG
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b6-f complex subunit VIIIH, 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], V [auth B]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
OPC
Query on OPC

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DA [auth N], EA [auth O], T [auth B], W [auth C](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
HEC
Query on HEC

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CA [auth N], S [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

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AA [auth N], BA [auth N], HA [auth P], Q [auth A], R [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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JA [auth R], Z [auth E]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
BNT
Query on BNT

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FA [auth O], U [auth B]2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE
C10 H10 Br2 O2
GHHZELQYJPWSMG-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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IA [auth Q], Y [auth D]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.276 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.587α = 90
b = 156.587β = 90
c = 361.786γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-02-26
    Changes: Database references, Other