4PD4 image
Entry Detail
PDB ID:
4PD4
Title:
Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action
Biological Source:
PDB Version:
Deposition Date:
2014-04-17
Release Date:
2014-06-11
Method Details:
Experimental Method:
Resolution:
3.04 Å
R-Value Free:
0.29
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 1, mitochondrial
Chain IDs:A
Chain Length:431
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 2, mitochondrial
Chain IDs:B
Chain Length:352
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b
Chain IDs:C
Chain Length:385
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome c1, heme protein, mitochondrial
Chain IDs:D
Chain Length:248
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit Rieske, mitochondrial
Chain IDs:E
Chain Length:185
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 6
Chain IDs:F
Chain Length:74
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 7
Chain IDs:G
Chain Length:126
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 8
Chain IDs:H
Chain Length:93
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Cytochrome b-c1 complex subunit 9
Chain IDs:I
Chain Length:57
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Igh protein
Chain IDs:J
Chain Length:127
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Description:Ig kappa chain V-V region HP 124E1
Chain IDs:K
Chain Length:107
Number of Molecules:1
Biological Source:Mus musculus
Primary Citation
Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action.
Nat Commun 5 4029 4029 (2014)
PMID: 24893593 DOI: 10.1038/ncomms5029

Abstact

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.

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