1L0L

structure of bovine mitochondrial cytochrome bc1 complex with a bound fungicide famoxadone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Famoxadone: The Role of Aromatic-Aromatic Interaction in Inhibition

Gao, X.Wen, X.Yu, C.A.Esser, L.Tsao, S.Quinn, B.Zhang, L.Yu, L.Xia, D.

(2003) Biochemistry 41: 11692-11702

  • DOI: https://doi.org/10.1021/bi026252p
  • Primary Citation of Related Structures:  
    1L0L, 1L0N

  • PubMed Abstract: 

    Ubiquinol cytochrome c oxido-reductase (EC. 1.10.2.2, bc1) is an integral membrane protein complex essential to cellular respiration. Structures of the 11-subunit mitochondrial bc1 complex were determined with and without the fungicide famoxadone. Specific inhibition by famoxadone is achieved through a coordinated optimization of aromatic-aromatic interactions where conformational rearrangements in famoxadone and in residues lining the inhibitor-binding pocket produce a network of aromatic-aromatic interactions that mimic the crystal lattice of benzene. The profound aromatic-aromatic interactions as supported by prior mutagenesis provide a structural basis for specific protein-ligand interaction in a hydrophobic environment. Dramatic conformational changes, both in cyt. b and ISP subunits in the inhibitor-protein complex, confer experimental evidence for a functional role of cytochrome b in the induced conformational arrest of ISP and allow the identification of a possible intrasubunit signal transduction pathway that controls the movement of ISP. These results support an inhibitory mechanism that is consistent with the requirement for ISP movement in the electron transfer of this complex.


  • Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I446Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2439Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome B379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein241Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00125
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT196Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP13272
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 14 kDa protein110Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C81Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 11 kDa protein78Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN78Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein62Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein56Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
L [auth C],
M [auth C],
O [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FMX
Query on FMX

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N [auth C]FAMOXADONE
C22 H18 N2 O4
PCCSBWNGDMYFCW-QFIPXVFZSA-N
FES
Query on FES

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P [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.094α = 90
b = 154.094β = 90
c = 591.839γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance