1SQV

Crystal Structure Analysis of Bovine Bc1 with UHDBT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 2.0 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, 1SQX

  • 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 only played crucial roles in elucidating the mechanism of bc(1) function but have also provided leads for the development of novel antibiotics ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase complex core protein I, mitochondrialA446Bos 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 2, mitochondrialB439Bos 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
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD241Bos taurusMutation(s): 0 
Gene Names: CYC1
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 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
EC: 1.10.2.2
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 complex 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 
UniProt
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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
UHD (Subject of Investigation/LOI)
Query on UHD

Download Ideal Coordinates CCD File 
N [auth C]6-HYDROXY-5-UNDECYL-1,3-BENZOTHIAZOLE-4,7-DIONE
C18 H25 N O3 S
QCWGBMWYLYKEIU-UHFFFAOYSA-N
 Ligand Interaction
UQ2 (Subject of Investigation/LOI)
Query on UQ2

Download Ideal Coordinates CCD File 
O [auth C]UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
Q [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.672α = 90
b = 153.672β = 90
c = 589.219γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary