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 2BCC | pdb_00002bcc

STIGMATELLIN-BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.317 (Depositor) 
  • R-Value Work: 
    0.284 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.284 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 234.1 kDa 
  • Atom Count: 15,754 
  • Modeled Residue Count: 2,000 
  • Deposited Residue Count: 2,048 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE380Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P18946 (Gallus gallus)
Explore P18946 
Go to UniProtKB:  P18946
Entity Groups
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UniProt GroupP18946
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE196Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE109Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE78Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence
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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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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE62Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U10

Query on U10



Download:Ideal Coordinates CCD File
M [auth C]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PEE

Query on PEE



Download:Ideal Coordinates CCD File
N [auth C],
S [auth E]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
Q [auth D]HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM



Download:Ideal Coordinates CCD File
K [auth C],
L [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SIG

Query on SIG



Download:Ideal Coordinates CCD File
O [auth C]STIGMATELLIN
C30 H42 O5
UDPIGEIYWVCFED-RBWCRZADSA-N
BOG

Query on BOG



Download:Ideal Coordinates CCD File
P [auth D]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
R [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.317 (Depositor) 
  • R-Value Work:  0.284 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.284 (Depositor) 
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
  • Version 2.1: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2026-09-30
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary