2D2C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.378 
  • R-Value Work: 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.USA 103: 69-74

  • DOI: 10.1073/pnas.0504909102

  • 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-methy ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b6
A, N
215Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex subunit 4
B, O
160Mastigocladus laminosusMutation(s): 0 
Gene 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
Apocytochrome f
C, P
289Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex iron-sulfur subunit
D, Q
179Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex subunit VI
E, R
32Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex subunit VII
F, S
35Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex subunit V
G, T
37Mastigocladus laminosusMutation(s): 0 
Gene 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
Cytochrome b6-f complex subunit VIII
H, U
29Mastigocladus laminosusMutation(s): 0 
Gene 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
BNT
Query on BNT

Download SDF File 
Download CCD File 
B, O
2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE
2,5-DIBROMO-3-METHYL-6-ISOPROPYLBENZOQUINONE, DBMIB
C10 H10 Br2 O2
GHHZELQYJPWSMG-UHFFFAOYSA-N
 Ligand Interaction
CLA
Query on CLA

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

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Download CCD File 
B, C, N, O
(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

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

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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

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Download CCD File 
E, R
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
HEC
Query on HEC

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Download CCD File 
A, N
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.276 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 156.587α = 90.00
b = 156.587β = 90.00
c = 361.786γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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