1NTZ

Crystal Structure of Mitochondrial Cytochrome bc1 Complex Bound with Ubiquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the quinone reduction in the bc(1) complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc(1) with bound substrate and inhibitors at the Q(i) site

Gao, X.Wen, X.Esser, L.Quinn, B.Yu, L.Yu, C.-A.Xia, D.

(2003) Biochemistry 42: 9067-9080

  • DOI: 10.1021/bi0341814
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cytochrome bc(1) is an integral membrane protein complex essential to cellular respiration and photosynthesis. The Q cycle reaction mechanism of bc(1) postulates a separated quinone reduction (Q(i)) and quinol oxidation (Q(o)) site. In a complete cat ...

    Cytochrome bc(1) is an integral membrane protein complex essential to cellular respiration and photosynthesis. The Q cycle reaction mechanism of bc(1) postulates a separated quinone reduction (Q(i)) and quinol oxidation (Q(o)) site. In a complete catalytic cycle, a quinone molecule at the Q(i) site receives two electrons from the b(H) heme and two protons from the negative side of the membrane; this process is specifically inhibited by antimycin A and NQNO. The structures of bovine mitochondrial bc(1) in the presence or absence of bound substrate ubiquinone and with either the bound antimycin A(1) or NQNO were determined and refined. A ubiquinone with its first two isoprenoid repeats and an antimycin A(1) were identified in the Q(i) pocket of the substrate and inhibitor bound structures, respectively; the NQNO, on the other hand, was identified in both Q(i) and Q(o) pockets in the inhibitor complex. The two inhibitors occupied different portions of the Q(i) pocket and competed with substrate for binding. In the Q(o) pocket, the NQNO behaves similarly to stigmatellin, inducing an iron-sulfur protein conformational arrest. Extensive binding interactions and conformational adjustments of residues lining the Q(i) pocket provide a structural basis for the high affinity binding of antimycin A and for phenotypes of inhibitor resistance. A two-water-mediated ubiquinone protonation mechanism is proposed involving three Q(i) site residues His(201), Lys(227), and Asp(228).


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial
A
446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
Find proteins for P31800 (Bos taurus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial
B
439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
EC: 1.10.2.2
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Find proteins for P00157 (Bos taurus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, mitochondrial
E
196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P13272 (Bos taurus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 11 kDa protein
H
78Bos taurusMutation(s): 0 
Gene Names: UQCRH
EC: 1.10.2.2
Find proteins for P00126 (Bos taurus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase 8 kDa protein
I
57Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
K
56Bos taurusMutation(s): 0 
Gene Names: UQCR11UQCR
EC: 1.10.2.2
Find proteins for P07552 (Bos taurus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
J
62Bos taurusMutation(s): 0 
Gene Names: UQCR10
EC: 1.10.2.2
Find proteins for P00130 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
cytochrome c1
D
241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex 14 kDa protein
F
110Bos taurusMutation(s): 0 
Gene Names: UQCRB
EC: 1.10.2.2
Find proteins for P00129 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
G
81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
EC: 1.10.2.2
Find proteins for P13271 (Bos taurus)
Go to UniProtKB:  P13271
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ2
Query on UQ2

Download CCD File 
C
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.828α = 90
b = 153.828β = 90
c = 596.671γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-07
    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