3H1I

Stigmatellin and antimycin bound cytochrome bc1 complex from chicken


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  
  • Also Cited By: 3CWB

  • 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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL
A, N
446Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX31 (Gallus gallus)
Go to UniProtKB:  D0VX31
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL
B, O
441Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX29 (Gallus gallus)
Go to UniProtKB:  D0VX29
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
380Gallus gallusMutation(s): 0 
Gene Names: MT-CYB (COB, CYTB, MTCYB)
Find proteins for P18946 (Gallus gallus)
Go to Gene View: MT-CYB
Go to UniProtKB:  P18946
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
D, Q
241Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX26 (Gallus gallus)
Go to UniProtKB:  D0VX26
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, R
196Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN
F, S
110Gallus gallusMutation(s): 0 
Find proteins for D0VX30 (Gallus gallus)
Go to UniProtKB:  D0VX30
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
G, T
81N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN
H, U
77N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
I, V
47Gallus gallusMutation(s): 0 
Gene Names: UQCRFS1
EC: 7.1.1.8
Find proteins for Q5ZLR5 (Gallus gallus)
Go to Gene View: UQCRFS1
Go to UniProtKB:  Q5ZLR5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN
J, W
61Gallus gallusMutation(s): 0 
EC: 1.10.2.2
Find proteins for D0VX27 (Gallus gallus)
Go to UniProtKB:  D0VX27
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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Download CCD File 
C, D, P, Q
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PLC
Query on PLC

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Download CCD File 
E, R
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
 Ligand Interaction
FES
Query on FES

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E, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

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D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SMA
Query on SMA

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C, P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
ANY
Query on ANY

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Download CCD File 
C, P
2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER
ANTIMYCIN
C29 H42 N2 O9
BSSBWOQOFMLGAF-GMRPKDQWSA-N
 Ligand Interaction
PEE
Query on PEE

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Download CCD File 
A, C, E, N, P
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
I, V
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 174.693α = 90.00
b = 181.666β = 90.00
c = 240.732γ = 90.00
Software Package:
Software NamePurpose
RAVEphasing
TFFCphasing
RAVEmodel building
CNSrefinement
SCALEPACKdata scaling
TFFCmodel building
DENZOdata reduction
ALMNphasing
ALMNmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance