2FYU

Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.

Esser, L., Gong, X., Yang, S., Yu, L., Yu, C.A., Xia, D.

(2006) Proc.Natl.Acad.Sci.Usa 103: 13045-13050

  • DOI: 10.1073/pnas.0601149103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation ...

    In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.

    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, mitochondrial
A
446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane protein
mpstruc		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
B
439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane protein
mpstruc		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 taurusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Membrane protein
mpstruc		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
D
241Bos taurusMutation(s): 0 
Gene Names: CYC1
Membrane protein
mpstruc		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: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial
E
196Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Membrane protein
mpstruc		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: 6
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein LOC616871
F
110Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane protein
mpstruc		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: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
G
81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane protein
mpstruc		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: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 11 kDa protein
H
78Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane protein
mpstruc		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: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial
I
78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Membrane protein
mpstruc		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: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
J
62Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane protein
mpstruc		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
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
K
56Bos taurusMutation(s): 0 
Gene Names: UQCR11 (UQCR)
Membrane protein
mpstruc		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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDN
Query on FDN
Download SDF File 
Download CCD File 
C
(5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE
5-(2,4-DIFLUORO-PHENYL)-5-METHYL-3-PHENYLAMINO-OXAZOLIDINE-2,4-DIONE
C16 H12 F2 N2 O3
OZZFJGCAYWBVBI-INIZCTEOSA-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: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.248 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.263α = 90.00
b = 154.263β = 90.00
c = 590.191γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-02-08 
  • Released Date: 2006-08-29 
  • Deposition Author(s): Xia, D., Esser, L.

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance