1KYO

YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c.

Lange, C.Hunte, C.

(2002) Proc Natl Acad Sci U S A 99: 2800-2805

  • DOI: 10.1073/pnas.052704699
  • Primary Citation of Related Structures:  
    1KYO

  • PubMed Abstract: 
  • Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover ...

    Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to integral membrane proteins. Specific and transient complexes need to be formed between the redox partners to ensure fast turnover. In respiration, the mobile electron carrier cytochrome c shuttles electrons from the cytochrome bc1 complex to cytochrome c oxidase. Despite extensive studies of this fundamental step of energy metabolism, the structures of the respective electron transfer complexes were not known. Here we present the crystal structure of the complex between cytochrome c and the cytochrome bc1 complex from Saccharomyces cerevisiae. The complex was crystallized with the help of an antibody fragment, and its structure was determined at 2.97-A resolution. Cytochrome c is bound to subunit cytochrome c1 of the enzyme. The tight and specific interactions critical for electron transfer are mediated mainly by nonpolar forces. The close spatial arrangement of the c-type hemes unexpectedly suggests a direct and rapid heme-to-heme electron transfer at a calculated rate of up to 8.3 x 10(6) s(-1). Remarkably, cytochrome c binds to only one recognition site of the homodimeric multisubunit complex. Interestingly, the occupancy of quinone in the Qi site is higher in the monomer with bound cytochrome c, suggesting a coordinated binding and reduction of both electron-accepting substrates. Obviously, cytochrome c reduction by the cytochrome bc1 complex can be regulated in response to respiratory conditions.


    Organizational Affiliation

    Max Planck Institute for Biophysics, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt am Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN IAL430Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2BM352Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME BCN385Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C1, HEME PROTEINDO248Saccharomyces cerevisiaeMutation(s): 0 
EC: 7.1.1.8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNITEP185Saccharomyces cerevisiaeMutation(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 REDUCTASE COMPLEX 17 KD PROTEINFQ74Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEINGR126Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-CHS93Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 9
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UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEINIT57Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
HEAVY CHAIN (VH) OF FV-FRAGMENTJU127Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
LIGHT CHAIN (VL) OF FV-FRAGMENTKV107Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C, ISO-1W108Saccharomyces cerevisiaeMutation(s): 1 
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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C, D, N, O, W
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA
Query on SMA

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

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E, P
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
WL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.224α = 90
b = 165.531β = 104.19
c = 195.889γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2002-02-05 
  • Released Date: 2002-03-06 
  • Deposition Author(s): Lange, C., Hunte, C.

Revision History 

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance