2IBZ

Yeast Cytochrome BC1 Complex with Stigmatellin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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
  • Primary Citation of Related Structures:  

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein 1
A
431Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COR1 (QCR1)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein 2
B
352Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR2 (COR2, UCR2)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COB (CYTB)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial precursor
D
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CYT1 (CTC1)
Membrane protein
mpstruct		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
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor
E
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RIP1
EC: 1.10.2.2
Membrane protein
mpstruct		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
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 17 kDa protein
H
74Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR6 (UCR6)
Membrane protein
mpstruct		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
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 14 kDa protein
F
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR7 (CRO1, UCR7)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
G
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR8
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 7.3 kDa protein
I
66Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR9 (UCR9)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Variable Heavy chain of antibody fragment
X
127Mus musculusMutation(s): 0 
Gene Names: Ighv3-6 (Gm16932)
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for P18531 (Mus musculus)
Go to UniProtKB:  P18531
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Variable Light chain of antibody fragment
Y
107Mus spMutation(s): 0 
Gene Names: Ig VL
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)		Protein: 
Cytochrome bc1
Find proteins for A0N6Y3 (Mus sp)
Go to UniProtKB:  A0N6Y3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES
Download SDF File 
Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA
Query on SMA
Download SDF File 
Download CCD File 
C
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
UQ6
Query on UQ6
Download SDF File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 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 = 90.00
b = 163.921β = 117.50
c = 147.276γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description