6FO2

CryoEM structure of bovine cytochrome bc1 with no ligand bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray and cryo-EM structures of inhibitor-bound cytochromebc1complexes for structure-based drug discovery.

Amporndanai, K.Johnson, R.M.O'Neill, P.M.Fishwick, C.W.G.Jamson, A.H.Rawson, S.Muench, S.P.Hasnain, S.S.Antonyuk, S.V.

(2018) IUCrJ 5: 200-210

  • DOI: https://doi.org/10.1107/S2052252518001616
  • Primary Citation of Related Structures:  
    5OKD, 6FO0, 6FO2, 6FO6

  • PubMed Abstract: 

    Cytochrome bc 1 , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome bc 1 from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome bc 1 that may be available from parasites, all efforts have been focused on homologous cytochrome bc 1 complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome bc 1 is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.


  • Organizational Affiliation

    Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA [auth N],
K [auth A]
480Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P31800 (Bos taurus)
Explore P31800 
Go to UniProtKB:  P31800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31800
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB [auth O],
L [auth B]
453Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23004 (Bos taurus)
Explore P23004 
Go to UniProtKB:  P23004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC [auth P],
M [auth C]
379Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00157 (Bos taurus)
Explore P00157 
Go to UniProtKB:  P00157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00157
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD [auth Q],
N [auth D]
325Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00125 (Bos taurus)
Explore P00125 
Go to UniProtKB:  P00125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00125
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE [auth R],
O [auth E]
274Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13272
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F [auth S],
P [auth F]
111Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00129 (Bos taurus)
Explore P00129 
Go to UniProtKB:  P00129
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00129
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8G [auth T],
Q [auth G]
82Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P13271 (Bos taurus)
Explore P13271 
Go to UniProtKB:  P13271
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13271
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialH [auth U],
R [auth H]
91Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00126 (Bos taurus)
Explore P00126 
Go to UniProtKB:  P00126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00126
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialI [auth V],
S [auth I]
16Bos taurusMutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P13272 (Bos taurus)
Explore P13272 
Go to UniProtKB:  P13272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13272
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9J [auth W],
T [auth J]
64Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00130 (Bos taurus)
Explore P00130 
Go to UniProtKB:  P00130
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00130
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom109158/B/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2018-05-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-12-11
    Changes: Other