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 

wwPDB Validation 3D Report Full Report


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.USA 99: 2800-2805

  • DOI: 10.1073/pnas.052704699

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
A, L
430Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: COR1 (QCR1)
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
B, M
352Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR2 (COR2, UCR2)
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B
C, N
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: COB (CYTB)
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN
D, O
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CYT1 (CTC1)
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07143
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
E, P
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RIP1
EC: 1.10.2.2
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08067
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
F, Q
74Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR6 (UCR6)
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00127
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
G, R
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR7 (CRO1, UCR7)
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
H, S
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR8
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
I, T
57Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR9 (UCR9)
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
HEAVY CHAIN (VH) OF FV-FRAGMENT
J, U
127N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
LIGHT CHAIN (VL) OF FV-FRAGMENT
K, V
107N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C, ISO-1
W
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
E, P
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
C, N
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 = 90.00
b = 165.531β = 104.19
c = 195.889γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance