3H1H

Cytochrome bc1 complex from chicken


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  
    2BCC, 3BCC, 3H1H, 3H1I, 3H1J, 1BCC

  • 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 ...

    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: 
    • Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial Bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-Bonding Pattern.
      Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.
      (2005) J Mol Biol 351: 573
    • The Structure of the Avian Mitochondrial Cytochrome bc1 Complex.
      Berry, E.A., Huang, L.S., Zhang, Z., Kim, S.H.
      (1999) J Bioenerg Biomembr 31: 177

    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 REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIALA, K [auth N]446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIALB, L [auth O]441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC, M [auth P]380Gallus gallusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIALD, N [auth Q]241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE, O [auth R]196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEINF, P [auth S]110Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-CG, Q [auth T]81Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEINH, R [auth U]77Gallus gallusMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI, S [auth V]47Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1RCJMB04_5b19
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEINJ, T [auth W]61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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AA [auth C], HA [auth D], VA [auth P], ZA [auth Q]CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
UQ (Subject of Investigation/LOI)
Query on UQ

Download Ideal Coordinates CCD File 
UA [auth P], Z [auth C]Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
 Ligand Interaction
PEE (Subject of Investigation/LOI)
Query on PEE

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BA [auth C], CA [auth C], DB [auth R], LA [auth E], OA [auth N], WA [auth P]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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GA [auth D], YA [auth Q]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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QA [auth P], RA [auth P], X [auth C], Y [auth C]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BOG (Subject of Investigation/LOI)
Query on BOG

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AB [auth Q], BB [auth Q], IA [auth D], JA [auth D], SA [auth P]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FES
Query on FES

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CB [auth R], KA [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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DA [auth C], XA [auth P]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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EA [auth C] , FA [auth C] , MA [auth N] , NA [auth N] , PA [auth N] , TA [auth P] , U [auth A] , V [auth A] , 
EA [auth C],  FA [auth C],  MA [auth N],  NA [auth N],  PA [auth N],  TA [auth P],  U [auth A],  V [auth A],  W [auth A]
Unknown ligand
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.16 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • 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
MLPHAREphasing
RAVEmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
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: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary