1BCC

CYTOCHROME BC1 COMPLEX FROM CHICKEN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 

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
  • Primary Citation of Related Structures:  
    3BCC, 3H1H, 3H1I, 3H1J, 1BCC, 2BCC

  • 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 gradien ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE A446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE B422Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL CYTOCHROME C OXIDOREDUCTASE C380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB, COB, CYTB, MTCYB
EC: 1.10.2.2
Find proteins for P18946 (Gallus gallus)
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Entity ID: 4
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE D241Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 5
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE E196Gallus gallusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 6
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE F109Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 7
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE G81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 8
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE H78Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 9
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE I33Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 10
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UBIQUINOL CYTOCHROME C OXIDOREDUCTASE J62Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U10
Query on U10
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C
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N		 Ligand Interaction
PEE
Query on PEE
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C, E
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O		 Ligand Interaction
HEM
Query on HEM
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C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
BOG
Query on BOG
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D
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
FES
Query on FES
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E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.59α = 90
b = 182.518β = 90
c = 240.573γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RAVEmodel building
CNSrefinement
RAVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-19
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-03-19
    Changes: Other
  • Version 1.4: 2014-10-29
    Changes: Non-polymer description
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary