1ZRT

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.300 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc (1): Comparison with its Mitochondrial and Chloroplast Counterparts.

Berry, E.A.Huang, L.S.Saechao, L.K.Pon, N.G.Valkova-Valchanova, M.Daldal, F.

(2004) Photosynth.Res. 81: 251-275

  • DOI: 10.1023/B:PRES.0000036888.18223.0e

  • PubMed Abstract: 
  • Ubihydroquinone: cytochrome (cyt)c oxidoreductase, or cyt bc (1), is a widespread, membrane integral enzyme that plays a crucial role during photosynthesis and respiration. It is one of the major contributors of the electrochemical proton gradient, w ...

    Ubihydroquinone: cytochrome (cyt)c oxidoreductase, or cyt bc (1), is a widespread, membrane integral enzyme that plays a crucial role during photosynthesis and respiration. It is one of the major contributors of the electrochemical proton gradient, which is subsequently used for ATP synthesis. The simplest form of the cyt bc (1) is found in bacteria, and it contains only the three ubiquitously conserved catalytic subunits: the Fe-S protein, cyt b and cyt c (1). Here we present a preliminary X-ray structure of Rhodobacter capsulatus cyt bc (1) at 3.8 A and compare it to the available structures of its homologues from mitochondria and chloroplast. Using the bacterial enzyme structure, we highlight the structural similarities and differences that are found among the three catalytic subunits between the members of this family of enzymes. In addition, we discuss the locations of currently known critical mutations, and their implications in terms of the cyt bc (1) catalysis.


    Organizational Affiliation

    Laurence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA, eaberry@lbl.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
437Rhodobacter capsulatusMutation(s): 0 
Gene Names: petB (cytB)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P0CY47 (Rhodobacter capsulatus)
Go to UniProtKB:  P0CY47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1
D, Q
258Rhodobacter capsulatusMutation(s): 0 
Gene Names: petC
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P0CY49 (Rhodobacter capsulatus)
Go to UniProtKB:  P0CY49
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit
E, R
191Rhodobacter capsulatusMutation(s): 0 
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 P0CY48 (Rhodobacter capsulatus)
Go to UniProtKB:  P0CY48
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

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

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

Download SDF File 
Download CCD File 
D, Q
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SMA
Query on SMA

Download SDF File 
Download CCD File 
C, P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.300 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.633α = 90.00
b = 154.360β = 113.57
c = 103.057γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance