6FO6

CryoEM structure of bovine cytochrome bc1 in complex with the anti-malarial inhibitor SCR0911


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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: 10.1107/S2052252518001616
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cytochrome <i>bc </i> <sub>1 </sub>, 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 cytochr ...

    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

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, R
274Bos taurusMutation(s): 0 
Gene Names: UQCRFS1
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Find proteins for P13272 (Bos taurus)
Go to UniProtKB:  P13272

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A, N
480Bos taurusMutation(s): 0 
Gene Names: UQCRC1
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1 in complex with azoxystrobin
Find proteins for P31800 (Bos taurus)
Go to UniProtKB:  P31800

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrial
B, O
453Bos taurusMutation(s): 0 
Gene Names: UQCRC2
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1 in complex with azoxystrobin
Find proteins for P23004 (Bos taurus)
Go to UniProtKB:  P23004

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C, P
379Bos taurusMutation(s): 0 
Gene Names: MT-CYBCOBCYTBMTCYB
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Find proteins for P00157 (Bos taurus)
Go to UniProtKB:  P00157

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial
D, Q
325Bos taurusMutation(s): 0 
Gene Names: CYC1
EC: 7.1.1.8
Find proteins for P00125 (Bos taurus)
Go to UniProtKB:  P00125

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
F, S
111Bos taurusMutation(s): 0 
Gene Names: UQCRB
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Find proteins for P00129 (Bos taurus)
Go to UniProtKB:  P00129

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8
G, T
82Bos taurusMutation(s): 0 
Gene Names: UQCRQ
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome
Find proteins for P13271 (Bos taurus)
Go to UniProtKB:  P13271

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6, mitochondrial
H, U
91Bos taurusMutation(s): 0 
Gene Names: UQCRH
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex I1III2IV1
Find proteins for P00126 (Bos taurus)
Go to UniProtKB:  P00126

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9
J, W
64Bos taurusMutation(s): 0 
Gene Names: UQCR10
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Super Complexes (Respirasome)
Protein: 
Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV
Find proteins for P00130 (Bos taurus)
Go to UniProtKB:  P00130
Small Molecules
Ligands 3 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
DY2
Query on DY2

Download CCD File 
C, P
7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]quinolin-4-ol
C23 H17 F3 N2 O3
ZZCQNODHORIHJA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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