2IBZ

Yeast Cytochrome BC1 Complex with Stigmatellin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome bc(1) Complex.

Lancaster, C.R.Hunte, C.Kelley, J.Trumpower, B.L.Ditchfield, R.

(2007) J Mol Biol 368: 197-208

  • DOI: 10.1016/j.jmb.2007.02.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here ...

    We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.


    Organizational Affiliation

    Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany. Roy.Lancaster@mpibp-frankfurt.mpg.de



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein 1
A
431Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Variable Heavy chain of antibody fragment
X
127Mus musculusMutation(s): 0 
Gene Names: variable domain antibody heavy chain
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Variable Light chain of antibody fragment
Y
107Mus musculusMutation(s): 0 
Gene Names: variable domain antibody light chain
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein 2
B
352Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
385Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial precursor
D
248Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07143

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor
E
185Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08067

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 17 kDa protein
H
74Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00127

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 14 kDa protein
F
127Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
G
94Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 7.3 kDa protein
I
66Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex III2IV
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ6
Query on UQ6

Download CCD File 
C
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
 Ligand Interaction
SMA
Query on SMA

Download CCD File 
C
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.473α = 90
b = 163.921β = 117.5
c = 147.276γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-09-12 
  • Released Date: 2007-03-20 
  • Deposition Author(s): Hunte, C.

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description