2FYN

Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.

Esser, L.Gong, X.Yang, S.Yu, L.Yu, C.A.Xia, D.

(2006) Proc.Natl.Acad.Sci.Usa 103: 13045-13050

  • DOI: 10.1073/pnas.0601149103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation ...

    In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein (ISP) between two redox sites constitutes a key component of the mechanism that achieves the separation of the two electrons in a substrate molecule at the quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is controlled so that only one electron enters the thermodynamically favorable chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound Q(o) site inhibitors revealed that the presence of inhibitors causes a bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the cd1 helix forms a major part of the ISP binding crater, any positional shift of this helix modulates the ability of cytochrome b to bind ISP. The analysis also suggests a mechanism for reversal of the ISP fixation when the shape complementarity is significantly reduced after a positional reorientation of the reaction product quinone. The importance of shape complementarity in this mechanism was confirmed by functional studies of bc(1) mutants and by a structure determination of the bacterial form of bc(1). A mechanism for the high fidelity of the bifurcated electron transfer is proposed.


    Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
A, D, G, J, M, P
445Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petB (fbcB)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for Q02761 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1
B, E, H, K, N, Q
269Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: petC (fbcC)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for Q02760 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, F, I, L, O, R
187Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: petA (fbcF)
EC: 7.1.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for Q02762 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02762
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download SDF File 
Download CCD File 
A, D, G, J, M, P
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
C, F, I, L, O, R
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, D, E, G, H, J, K, M, N, P, Q
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 
A, D, G, J, M, P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 351.300α = 90.00
b = 147.130β = 103.94
c = 160.830γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOLREPphasing
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-02-08 
  • Released Date: 2006-08-29 
  • Deposition Author(s): Esser, L., Xia, D.

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance