4PD4

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action.

Birth, D.Kao, W.C.Hunte, C.

(2014) Nat Commun 5: 4029-4029

  • DOI: 10.1038/ncomms5029
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Atovaquone, a substituted hydroxynaphthoquinone, is a potent antimalarial drug that acts by inhibiting the parasite's mitochondrial cytochrome bc1 complex (cyt bc1). Mutations in cyt bc1 confer atovaquone resistance. Here we describe the X-ray struct ...

    Atovaquone, a substituted hydroxynaphthoquinone, is a potent antimalarial drug that acts by inhibiting the parasite's mitochondrial cytochrome bc1 complex (cyt bc1). Mutations in cyt bc1 confer atovaquone resistance. Here we describe the X-ray structure of mitochondrial cyt bc1 from Saccharomyces cerevisiae with atovaquone bound in the catalytic Qo site, at 3.0-Å resolution. A polarized H-bond to His181 of the Rieske protein in cyt bc1 traps the ionized hydroxyl group of the drug. Side chains of highly conserved cytochrome b residues establish multiple non-polar interactions with the napththoquinone group, whereas less-conserved residues are in contact with atovaquone's cyclohexyl-chlorophenyl tail. Our structural analysis reveals the molecular basis of atovaquone's broad target spectrum, species-specific efficacies and acquired resistances, and may aid drug development to control the spread of resistant parasites.


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, ZMBZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 1, mitochondrial
A
431Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COR1QCR1YBL045CYBL0403
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 III2IV
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07256

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 2, mitochondrial
B
352Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR2COR2UCR2YPR191WP9677.6
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 III2IV
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07257

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
C
385Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: COBCYTBQ0105
EC: 7.1.1.8
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 III2IV
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00163

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1, heme protein, mitochondrial
D
248Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CYT1CTC1YOR065WYOR29-16
EC: 7.1.1.8
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07143

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RIP1YEL024W
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08067

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 6
F
74Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR6UCR6YFR033C
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00127

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 7
G
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR7CRO1UCR7YDR529CD9719.32
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 III2IV
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00128

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 8
H
93Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR8YJL166WJ0526
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 III2IV
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08525

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b-c1 complex subunit 9
I
57Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QCR9UCR9YGR183C
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex III (Cytochrome bc1)
Protein: 
Cytochrome bc1
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22289

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Igh protein
J
127Mus musculusMutation(s): 0 
Gene Names: Igh
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ig kappa chain V-V region HP 124E1
K
107Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download CCD File 
C
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
3PH
Query on 3PH

Download CCD File 
A, C, E
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ6
Query on UQ6

Download CCD File 
C
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
 Ligand Interaction
UMQ
Query on UMQ

Download CCD File 
A
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
AOQ
Query on AOQ

Download CCD File 
C
2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
C22 H19 Cl O3
KUCQYCKVKVOKAY-CTYIDZIISA-N
 Ligand Interaction
FES
Query on FES

Download CCD File 
E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.26α = 90
b = 150.88β = 115.18
c = 143.09γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyCRC 746, CRC 992
Excellence Initiative of the German Federal and State GovernmentsGermanyEXC 294 BIOSS

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2016-04-20
    Changes: Non-polymer description
  • Version 1.4: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence