7JG6

Cryo-EM structure of bedaquiline-free Mycobacterium smegmatis ATP synthase rotational state 2 (backbone model)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline.

Guo, H.Courbon, G.M.Bueler, S.A.Mai, J.Liu, J.Rubinstein, J.L.

(2021) Nature 589: 143-147

  • DOI: https://doi.org/10.1038/s41586-020-3004-3
  • Primary Citation of Related Structures:  
    7JG5, 7JG6, 7JG7, 7JG8, 7JG9, 7JGA, 7JGB, 7JGC

  • PubMed Abstract: 

    Tuberculosis-the world's leading cause of death by infectious disease-is increasingly resistant to current first-line antibiotics 1 . The bacterium Mycobacterium tuberculosis (which causes tuberculosis) can survive low-energy conditions, allowing infections to remain dormant and decreasing their susceptibility to many antibiotics 2 . Bedaquiline was developed in 2005 from a lead compound identified in a phenotypic screen against Mycobacterium smegmatis 3 . This drug can sterilize even latent M. tuberculosis infections 4 and has become a cornerstone of treatment for multidrug-resistant and extensively drug-resistant tuberculosis 1,5,6 . Bedaquiline targets the mycobacterial ATP synthase 3 , which is an essential enzyme in the obligate aerobic Mycobacterium genus 3,7 , but how it binds the intact enzyme is unknown. Here we determined cryo-electron microscopy structures of M. smegmatis ATP synthase alone and in complex with bedaquiline. The drug-free structure suggests that hook-like extensions from the α-subunits prevent the enzyme from running in reverse, inhibiting ATP hydrolysis and preserving energy in hypoxic conditions. Bedaquiline binding induces large conformational changes in the ATP synthase, creating tight binding pockets at the interface of subunits a and c that explain the potency of this drug as an antibiotic for tuberculosis.


  • Organizational Affiliation

    Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B
548Mycolicibacterium smegmatisMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R202 
Go to UniProtKB:  A0R202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R202
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha548Mycolicibacterium smegmatisMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R202 
Go to UniProtKB:  A0R202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R202
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
475Mycolicibacterium smegmatisMutation(s): 0 
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R200 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R200 
Go to UniProtKB:  A0R200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R200
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain307Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R201 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R201 
Go to UniProtKB:  A0R201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R201
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain121Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R1Z9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R1Z9 
Go to UniProtKB:  A0R1Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R1Z9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aI [auth a]252Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R206 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R206 
Go to UniProtKB:  A0R206
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R206
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bJ [auth b]170Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R204 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R204 
Go to UniProtKB:  A0R204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R204
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit b-deltaK [auth d]445Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R203 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R203 
Go to UniProtKB:  A0R203
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R203
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c86Mycolicibacterium smegmatisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R205 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R205 
Go to UniProtKB:  A0R205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R205
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTcryoSPARC2.11
RECONSTRUCTIONcryoSPARC2.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT162186
Canadian Institutes of Health Research (CIHR)CanadaPJT156261

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references