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 

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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
  • Primary Citation of Related Structures:  
    4PD4

  • 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 structure of mitochondrial cyt bc1 from Saccharomyces cerevisiae with atovaquone bound in the catalytic Qo site, at 3 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA431Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COR1QCR1YBL045CYBL0403
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB352Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR2COR2UCR2YPR191WP9677.6
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome bC385Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: COBCYTBQ0105
EC: 7.1.1.8
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CYT1CTC1YOR065WYOR29-16
EC: 7.1.1.8
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIP1YEL024W
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6F74Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR6UCR6YFR033C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7G126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR7CRO1UCR7YDR529CD9719.32
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8H93Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR8YJL166WJ0526
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9I57Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: QCR9UCR9YGR183C
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Igh proteinJ127Mus musculusMutation(s): 0 
Gene Names: Igh
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ig kappa chain V-V region HP 124E1K107Mus musculusMutation(s): 0 
Find proteins for P01647 (Mus musculus)
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

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Q [auth C]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
3PH
Query on 3PH

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M [auth A], S [auth C], V [auth E]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
HEM
Query on HEM

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N [auth C], O [auth C], T [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UQ6
Query on UQ6

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R [auth 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

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L [auth A]UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
AOQ
Query on AOQ

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P [auth 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

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U [auth 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

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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  (Full details and data files)

  • 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