1ZRT

Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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Ligand Structure Quality Assessment 


This is version 2.0 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bA [auth C],
D [auth P]
437Rhodobacter capsulatusMutation(s): 0 
Gene Names: petBcytBRCAP_rcc02769
Membrane Entity: Yes 
UniProt
Find proteins for P0CY47 (Rhodobacter capsulatus)
Explore P0CY47 
Go to UniProtKB:  P0CY47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CY47
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1B [auth D],
E [auth Q]
258Rhodobacter capsulatusMutation(s): 0 
Gene Names: petCRCAP_rcc02770
Membrane Entity: Yes 
UniProt
Find proteins for P0CY49 (Rhodobacter capsulatus)
Explore P0CY49 
Go to UniProtKB:  P0CY49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CY49
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunitC [auth E],
F [auth R]
191Rhodobacter capsulatusMutation(s): 0 
Gene Names: petAfbcFRCAP_rcc02768
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P0CY48 (Rhodobacter capsulatus)
Explore P0CY48 
Go to UniProtKB:  P0CY48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CY48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
L [auth D],
S [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth C],
H [auth C],
N [auth P],
O [auth P]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SMA (Subject of Investigation/LOI)
Query on SMA

Download Ideal Coordinates CCD File 
I [auth C],
P
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
PG6
Query on PG6

Download Ideal Coordinates CCD File 
T [auth Q]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
M [auth E],
U [auth R]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
J [auth C],
K [auth C],
Q [auth P],
R [auth P]
Unknown ligand
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • 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
PHENIXrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK44842
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM38237

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
  • Version 2.0: 2022-08-17
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary