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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN IA446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2B439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome BC379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme proteinD241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNITE196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
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 14 kDa proteinF110Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-CG81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 11 kDa proteinH78Bos taurusMutation(s): 0 
Gene Names: UQCRH
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEINI78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 7.2 kDa proteinJ62Bos taurusMutation(s): 0 
Gene Names: UQCR10
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome C reductase complex 6.4 kDa proteinK56Bos taurusMutation(s): 0 
Gene Names: UQCR11UQCR
EC: 1.10.2.2
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
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
 Ligand Interaction
FMX (Subject of Investigation/LOI)
Query on FMX

Download Ideal Coordinates CCD File 
N [auth C]FAMOXADONE
C22 H18 N2 O4
PCCSBWNGDMYFCW-QFIPXVFZSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
P [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
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