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 2.0 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:  
    2IBZ, 2JBL

  • 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 the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex ...

    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 LengthOrganismDetailsImage
Ubiquinol-cytochrome-c reductase complex core protein 1A431Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome-c reductase complex core protein 2B352Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC385Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial precursorD248Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursorE185Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 17 kDa proteinF [auth H]74Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 14 kDa proteinG [auth F]127Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-CH [auth G]94Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex 7.3 kDa proteinI66Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Variable Heavy chain of antibody fragmentJ [auth X]127Mus musculusMutation(s): 0 
Gene Names: variable domain antibody heavy chainIghv3-6Gm16932
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Variable Light chain of antibody fragmentK [auth Y]107Mus musculusMutation(s): 0 
Gene Names: variable domain antibody light chain
UniProt
Find proteins for A0N6Y3 (Mus sp)
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
L [auth C], M [auth C], P [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
UQ6 (Subject of Investigation/LOI)
Query on UQ6

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N [auth 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 (Subject of Investigation/LOI)
Query on SMA

Download Ideal Coordinates CCD File 
O [auth C]STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
FES
Query on FES

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Q [auth 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

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary