4PD4 | pdb_00004pd4

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 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.7 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: https://doi.org/10.1038/ncomms5029
  • Primary Citation 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 3.0-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
    • 1] Institute for Biochemistry and Molecular Biology, ZMBZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Stefan-Meier-Strasse 17, 79104 Freiburg, Germany [2] Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 251.15 kDa 
  • Atom Count: 17,646 
  • Modeled Residue Count: 2,185 
  • Deposited Residue Count: 2,185 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial431Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P07256
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UniProt GroupP07256
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial352Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07257 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P07257
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UniProt GroupP07257
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b385Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P00163 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00163
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial248Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 7.1.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP07143
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial185Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP08067
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 674Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00127
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7126Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00128
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 893Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P08525 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP08525
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 957Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P22289 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Igh protein127Mus musculusMutation(s): 0 
Gene Names: Igh
UniProt
Find proteins for Q53VQ5 (Mus musculus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig kappa chain V-V region HP 124E1107Mus musculusMutation(s): 0 
UniProt
Find proteins for P01647 (Mus musculus)
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
Q [auth C]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH

Query on 3PH



Download:Ideal Coordinates CCD File
M [auth A],
S [auth C],
V [auth E]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
N [auth C],
O [auth C],
T [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ6

Query on UQ6



Download:Ideal Coordinates CCD File
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
UMQ

Query on UMQ



Download:Ideal Coordinates CCD File
L [auth A]UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
AOQ

Query on AOQ



Download:Ideal Coordinates CCD File
P [auth C]2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione
C22 H19 Cl O3
KUCQYCKVKVOKAY-CTYIDZIISA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
U [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free:  0.297 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.270 (DCC) 
  • R-Value Observed: 0.269 (Depositor) 
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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Ligand Structure Quality Assessment 


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
  • Version 1.6: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.7: 2024-11-20
    Changes: Structure summary