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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1038/33612
  • Primary Citation of Related Structures:  
    1BCC, 2BCC, 3BCC, 3H1H, 3H1I, 3H1J

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P31800 (Bos taurus)
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE422Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE380Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P18946 (Gallus gallus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P00125 (Bos taurus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE196Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P13272 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE109Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P00129 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE78Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE33Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE62Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
Find proteins for P00130 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10

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M [auth C]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PEE
Query on PEE

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N [auth C],
S [auth E]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEM
Query on HEM

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K [auth C],
L [auth C],
Q [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SIG
Query on SIG

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O [auth C]STIGMATELLIN
C30 H42 O5
UDPIGEIYWVCFED-RBWCRZADSA-N
BOG
Query on BOG

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P [auth D]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES
Query on FES

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R [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 2.0: 2023-08-23
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary