1KB9

YEAST CYTOCHROME BC1 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

SPECIFIC ROLES OF PROTEIN-PHOSPHOLIPID INTERACTIONS IN THE YEAST CYTOCHROME BC1 COMPLEX STRUCTURE

Lange, C.Nett, J.H.Trumpower, B.L.Hunte, C.

(2001) EMBO J. 20: 6591-6600

  • DOI: 10.1093/emboj/20.23.6591

  • PubMed Abstract: 
  • Biochemical data have shown that specific, tightly bound phospholipids are essential for activity of the cytochrome bc1 complex (QCR), an integral membrane protein of the respiratory chain. However, the structure and function of such phospholipids ar ...

    Biochemical data have shown that specific, tightly bound phospholipids are essential for activity of the cytochrome bc1 complex (QCR), an integral membrane protein of the respiratory chain. However, the structure and function of such phospholipids are not yet known. Here we describe five phospholipid molecules and one detergent molecule in the X-ray structure of yeast QCR at 2.3 A resolution. Their individual binding sites suggest specific roles in facilitating structural and functional integrity of the enzyme. Interestingly, a phosphatidylinositol molecule is bound in an unusual interhelical position near the flexible linker region of the Rieske iron-sulfur protein. Two possible proton uptake pathways at the ubiquinone reduction site have been identified: the E/R and the CL/K pathway. Remarkably, cardiolipin is positioned at the entrance to the latter. We propose that cardiolipin ensures structural integrity of the proton-conducting protein environment and takes part directly in proton uptake. Site-directed mutagenesis of ligating residues confirmed the importance of the phosphatidylinositol- and cardiolipin-binding sites.


    Related Citations: 
    • Structure Of The Yeast Cytochrome Bc1 Complex Co-Crystallized With An Antibody Fv-Fragment
      Hunte, C.,Koepke, J.,Lange, C.,Rossmanith, T.,Michel, H.
      (2000) Structure 8: 669


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60528 Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
A
431Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: COR1 (QCR1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
352Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR2 (COR2, UCR2)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B
C
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: COB (CYTB)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN
D
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CYT1 (CTC1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RIP1
EC: 1.10.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
74Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR6 (UCR6)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR7 (CRO1, UCR7)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR8
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
55Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: QCR9 (UCR9)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
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
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
107N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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

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Download CCD File 
C
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
 Ligand Interaction
FES
Query on FES

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

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Download CCD File 
C
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL
C43 H80 O13 P
PDLAMJKMOKWLAJ-OJERQSHOSA-M
 Ligand Interaction
UMQ
Query on UMQ

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Download CCD File 
A
UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
HEM
Query on HEM

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

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Download CCD File 
A
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
 Ligand Interaction
SMA
Query on SMA

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Download CCD File 
C
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
UQ6
Query on UQ6

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Download CCD File 
C
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 214.473α = 90.00
b = 163.921β = 117.50
c = 147.276γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-08-31
    Type: Non-polymer description