2BCC

STIGMATELLIN-BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Electron Transfer by Domain Movement in Cytochrome Bc1

Zhang, Z.Huang, L.Shulmeister, V.M.Chi, Y.I.Kim, K.K.Hung, L.W.Crofts, A.R.Berry, E.A.Kim, S.H.

(1998) Nature 392: 677-684

  • DOI: 10.1038/33612
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The cytochrome bc1 is one of the three major respiratory enzyme complexes residing in the inner mitochondrial membrane. Cytochrome bc1 transfers electrons from ubiquinol to cytochrome c and uses the energy thus released to form an electrochemical gra ...

    The cytochrome bc1 is one of the three major respiratory enzyme complexes residing in the inner mitochondrial membrane. Cytochrome bc1 transfers electrons from ubiquinol to cytochrome c and uses the energy thus released to form an electrochemical gradient across the inner membrane. Our X-ray crystal structures of the complex from chicken, cow and rabbit in both the presence and absence of inhibitors of quinone oxidation, reveal two different locations for the extrinsic domain of one component of the enzyme, an iron-sulphur protein. One location is close enough to the supposed quinol oxidation site to allow reduction of the Fe-S protein by ubiquinol. The other site is close enough to cytochrome c1 to allow oxidation of the Fe-S protein by the cytochrome. As neither location will allow both reactions to proceed at a suitable rate, the reaction mechanism must involve movement of the extrinsic domain of the Fe-S component in order to shuttle electrons from ubiquinol to cytochrome c1. Such a mechanism has not previously been observed in redox protein complexes.


    Related Citations: 
    • Pathways for proton release during ubihydroquinone oxidation by the bc(1) complex.
      Crofts, A.R., Hong, S., Ugulava, N., Barquera, B., Gennis, R., Guergova-Kuras, M., Berry, E.A.
      (1999) Proc Natl Acad Sci U S A 96: 10021

    Organizational Affiliation

    E. O. Lawrence Berkeley National Laboratory, University of California, 94720, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
A
446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
B
422Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1 in complex with azoxystrobin
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
C
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
EC: 1.10.2.2
Find proteins for P18946 (Gallus gallus)
Go to UniProtKB:  P18946

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
D
241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
E
196Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1 in complex with azoxystrobin
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
F
109Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
G
81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
H
78Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1 in complex with azoxystrobin
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
I
33Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
J
62Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

Download CCD File 
C
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
PEE
Query on PEE

Download CCD File 
C, E
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
HEM
Query on HEM

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

Download CCD File 
C
STIGMATELLIN
C30 H42 O5
UDPIGEIYWVCFED-RBWCRZADSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-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: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.284 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.46α = 90
b = 182.45β = 90
c = 241.33γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
ALMNmodel building
TFFCmodel building
RAVEmodel building
CNSrefinement
CCP4phasing
TFFCphasing
RAVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2013-05-22
    Changes: Database references
  • Version 1.4: 2014-10-29
    Changes: Non-polymer description
  • Version 1.5: 2017-10-04
    Changes: Refinement description