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
  • Structures With Same Primary Citation

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1D, 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
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunitE, R191Rhodobacter capsulatusMutation(s): 0 
Gene Names: petAfbcF
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
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome bC, P437Rhodobacter capsulatusMutation(s): 0 
Gene Names: petBcytB
EC: 1.10.2.2
Find proteins for P0CY47 (Rhodobacter capsulatus)
Explore P0CY47 
Go to UniProtKB:  P0CY47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

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

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

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

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

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Entry History 

Deposition Data

Revision History 

  • 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