6WTD

Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of Bedaquiline bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bedaquiline inhibits the yeast and human mitochondrial ATP synthases.

Luo, M.Zhou, W.Patel, H.Srivastava, A.P.Symersky, J.Bonar, M.M.Faraldo-Gomez, J.D.Liao, M.Mueller, D.M.

(2020) Commun Biol 3: 452-452

  • DOI: https://doi.org/10.1038/s42003-020-01173-z
  • Primary Citation of Related Structures:  
    6WTD

  • PubMed Abstract: 

    Bedaquiline (BDQ, Sirturo) has been approved to treat multidrug resistant forms of Mycobacterium tuberculosis. Prior studies suggested that BDQ was a selective inhibitor of the ATP synthase from M. tuberculosis. However, Sirturo treatment leads to an increased risk of cardiac arrhythmias and death, raising the concern that this adverse effect results from inhibition at a secondary site. Here we show that BDQ is a potent inhibitor of the yeast and human mitochondrial ATP synthases. Single-particle cryo-EM reveals that the site of BDQ inhibition partially overlaps with that of the inhibitor oligomycin. Molecular dynamics simulations indicate that the binding mode of BDQ to this site is similar to that previously seen for a mycobacterial enzyme, explaining the observed lack of selectivity. We propose that derivatives of BDQ ought to be made to increase its specificity toward the mycobacterial enzyme and thereby reduce the side effects for patients that are treated with Sirturo.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA, 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 9, mitochondrial76Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P61829
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UniProt GroupP61829
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase protein 8K [auth 8]48Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00856 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00856
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aL [auth X]249Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00854 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP00854
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit 4, mitochondrialM [auth Z]209Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05626 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP05626
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit d, mitochondrialN [auth 7]173Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P30902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit f, mitochondrialO [auth U]95Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q06405 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ06405
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit J, mitochondrialP [auth J]37Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P81450 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A [auth K]
B [auth L]
C [auth M]
D [auth N]
E [auth O]
A [auth K],
B [auth L],
C [auth M],
D [auth N],
E [auth O],
F [auth P],
G [auth Q],
H [auth R],
I [auth S],
J [auth T]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Library of Medicine (NIH/NLM)United StatesR01GM66223
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM131731

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references