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 

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

  • Primary Citation of Related Structures:  
  • Also Cited By: 1SQV

  • 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. Sp ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
A
446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Find proteins for P31800 (Bos taurus)
Go to Gene View: UQCRC1
Go to UniProtKB:  P31800
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
B
439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Find proteins for P23004 (Bos taurus)
Go to Gene View: UQCRC2
Go to UniProtKB:  P23004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome B
C
379Bos taurusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P00157 (Bos taurus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P00157
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein
D
241Bos taurusMutation(s): 0 
Gene Names: CYC1
Find proteins for P00125 (Bos taurus)
Go to Gene View: CYC1
Go to UniProtKB:  P00125
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
E
196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 14 kDa protein
F
110Bos taurusMutation(s): 0 
Gene Names: UQCRB
Find proteins for P00129 (Bos taurus)
Go to Gene View: UQCRB
Go to UniProtKB:  P00129
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
G
81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Find proteins for P13271 (Bos taurus)
Go to Gene View: UQCRQ
Go to UniProtKB:  P13271
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 11 kDa protein
H
78Bos taurusMutation(s): 0 
Gene Names: UQCRH
Find proteins for P00126 (Bos taurus)
Go to Gene View: UQCRH
Go to UniProtKB:  P00126
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE 8 KDA PROTEIN
I
78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2
Find proteins for P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
J
62Bos taurusMutation(s): 0 
Gene Names: UQCR10
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
K
56Bos taurusMutation(s): 0 
Gene Names: UQCR11 (UQCR)
Find proteins for P07552 (Bos taurus)
Go to Gene View: UQCR11
Go to UniProtKB:  P07552
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMX
Query on FMX

Download SDF File 
Download CCD File 
C
FAMOXADONE
5-METHYL-5-(4-PHENOXYPHENYL)-3-(PHENYLAMINO)-2,4-OXAZOLIDINEDIONE
C22 H18 N2 O4
PCCSBWNGDMYFCW-QFIPXVFZSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.259 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.094α = 90.00
b = 154.094β = 90.00
c = 591.839γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4phasing
SCALEPACKdata scaling
DENZOdata reduction
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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