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 
  • R-Value Observed: 0.249 

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 U S A 103: 13045-13050

  • DOI: 10.1073/pnas.0601149103
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrialA446Bos taurusMutation(s): 0 
Gene Names: UQCRC1
EC: 1.10.2.2
Find proteins for P31800 (Bos taurus)
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrialB439Bos taurusMutation(s): 0 
Gene Names: UQCRC2
EC: 1.10.2.2
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome bC379Bos taurusMutation(s): 0 
Gene Names: MT-CYB, COB, CYTB, MTCYB
Find proteins for P00157 (Bos taurus)
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrialD241Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Find proteins for P00125 (Bos taurus)
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrialE196Bos 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: 6
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein LOC616871F110Bos taurusMutation(s): 0 
Gene Names: UQCRB
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-CG81Bos taurusMutation(s): 0 
Gene Names: UQCRQ
EC: 1.10.2.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 11 kDa proteinH78Bos taurusMutation(s): 0 
Gene Names: UQCRH
EC: 1.10.2.2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrialI78Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 7.2 kDa proteinJ62Bos taurusMutation(s): 0 
Gene Names: UQCR10
EC: 1.10.2.2
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase complex 6.4 kDa proteinK56Bos taurusMutation(s): 0 
Gene Names: UQCR11, UQCR
EC: 1.10.2.2
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  • Reference Sequence
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
FDN
Query on FDN
Download CCD File 
C
(5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE
C16 H12 F2 N2 O3
OZZFJGCAYWBVBI-INIZCTEOSA-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: 2.26 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.263α = 90
b = 154.263β = 90
c = 590.191γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance