1ZRT

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.300 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1ZRT

  • 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, which is subsequently used for ATP synthesis ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b C, P437Rhodobacter capsulatusMutation(s): 0 
Gene Names: petB, cytB
EC: 1.10.2.2
Find proteins for P0CY47 (Rhodobacter capsulatus)
Explore P0CY47 
Go to UniProtKB:  P0CY47
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1 D, Q258Rhodobacter capsulatusMutation(s): 0 
Gene Names: petC
EC: 1.10.2.2
Find proteins for P0CY49 (Rhodobacter capsulatus)
Explore P0CY49 
Go to UniProtKB:  P0CY49
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit E, R191Rhodobacter capsulatusMutation(s): 0 
Gene Names: petA, fbcF
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P0CY48 (Rhodobacter capsulatus)
Explore P0CY48 
Go to UniProtKB:  P0CY48
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.300 
  • R-Value Observed: 0.300 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.633α = 90
b = 154.36β = 113.57
c = 103.057γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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