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 

Starting Model: experimental
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This is version 2.1 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
A, L
430Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07256
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
B, M
352Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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UniProt GroupP07257
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME B
C, N
385Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupP00163
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C1, HEME PROTEIN
D, O
248Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
E, P
185Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
F, Q
74Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
G, R
126Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
H, S
93Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
I, T
57Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
HEAVY CHAIN (VH) OF FV-FRAGMENT
J, U
127Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LIGHT CHAIN (VL) OF FV-FRAGMENT
K, V
107Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C, ISO-1108Saccharomyces cerevisiaeMutation(s): 1 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth N]
DA [auth N]
FA [auth O]
HA [auth W]
AA [auth D],
CA [auth N],
DA [auth N],
FA [auth O],
HA [auth W],
X [auth C],
Y [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SMA
Query on SMA

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EA [auth N],
Z [auth C]
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
FES
Query on FES

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BA [auth E],
GA [auth P]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
W
L-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

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description