1SQX

Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex.

Esser, L.Quinn, B.Li, Y.F.Zhang, M.Elberry, M.Yu, L.Yu, C.A.Xia, D.

(2004) J.Mol.Biol. 341: 281-302

  • DOI: 10.1016/j.jmb.2004.05.065
  • Primary Citation of Related Structures:  1SQB, 1SQP, 1SQQ, 1SQV

  • PubMed Abstract: 
  • Cytochrome bc(1) is an integral membrane protein complex essential for cellular respiration and photosynthesis; it couples electron transfer from quinol to cytochrome c to proton translocation across the membrane. Specific bc(1) inhibitors have not o ...

    Cytochrome bc(1) is an integral membrane protein complex essential for cellular respiration and photosynthesis; it couples electron transfer from quinol to cytochrome c to proton translocation across the membrane. Specific bc(1) inhibitors have not only played crucial roles in elucidating the mechanism of bc(1) function but have also provided leads for the development of novel antibiotics. Crystal structures of bovine bc(1) in complex with the specific Q(o) site inhibitors azoxystrobin, MOAS, myxothiazol, stigmatellin and 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole were determined. Interactions, conformational changes and possible mechanisms of resistance, specific to each inhibitor, were defined. Residues and secondary structure elements that are capable of discriminating different classes of Q(o) site inhibitors were identified for the cytochrome b subunit. Directions in the displacement of the cd1 helix of cytochrome b subunit in response to various Q(o) site inhibitors were correlated to the binary conformational switch of the extrinsic domain of the iron-sulfur protein subunit. The new structural information, together with structures previously determined, provide a basis that, combined with biophysical and mutational data, suggest a modification to the existing classification of bc(1) inhibitors. bc(1) inhibitors are grouped into three classes: class P inhibitors bind to the Q(o) site, class N inhibitors bind to the Q(i) site and the class PN inhibitors target both sites. Class P contains two subgroups, Pm and Pf, that are distinct by their ability to induce mobile or fixed conformation of iron-sulfur protein.


    Related Citations: 
    • 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.,Esser, L.,Tsao, S.,Quinn, B.,Zhang, L.,Yu, L.,Xia, D.
      (2002) Biochemistry 41: 11692
    • Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.
      Xia, D.,Yu, C.A.,Kim, H.,Xia, J.Z.,Kachurin, A.M.,Zhang, L.,Yu, L.,Deisenhofer, J.
      (1997) Science 277: 60


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
A
446Bos taurusGene Names: UQCRC1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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, mitochondrial precursor
B
439Bos taurusGene Names: UQCRC2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P23004 (Bos taurus)
Go to Gene View: UQCRC2
Go to UniProtKB:  P23004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
379Bos taurusGene Names: MT-CYB (COB, CYTB, MTCYB)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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, mitochondrial
E
196Bos taurusGene Names: UQCRFS1
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 P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
D
241Bos taurusGene Names: CYC1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00125 (Bos taurus)
Go to Gene View: CYC1
Go to UniProtKB:  P00125
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 14 kDa protein
G
81Bos taurusGene Names: UQCRQ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P13271 (Bos taurus)
Go to Gene View: UQCRQ
Go to UniProtKB:  P13271
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
I
78Bos taurusGene Names: UQCRFS1
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 P13272 (Bos taurus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  P13272
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 11 kDa protein
F
110Bos taurusGene Names: UQCRB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00129 (Bos taurus)
Go to Gene View: UQCRB
Go to UniProtKB:  P00129
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
K
56Bos taurusGene Names: UQCR11 (UQCR)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P07552 (Bos taurus)
Go to Gene View: UQCR11
Go to UniProtKB:  P07552
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
H
78Bos taurusGene Names: UQCRH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00126 (Bos taurus)
Go to Gene View: UQCRH
Go to UniProtKB:  P00126
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
J
62Bos taurusGene Names: UQCR10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00130 (Bos taurus)
Go to Gene View: UQCR10
Go to UniProtKB:  P00130
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
UQ2
Query on UQ2

Download SDF File 
Download CCD File 
C
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.233 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.385α = 90.00
b = 154.385β = 90.00
c = 590.271γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance