8J58

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase Fo in the apo-form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 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

Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587.

Zhang, Y.Lai, Y.Zhou, S.Ran, T.Zhang, Y.Zhao, Z.Feng, Z.Yu, L.Xu, J.Shi, K.Wang, J.Pang, Y.Li, L.Chen, H.Guddat, L.W.Gao, Y.Liu, F.Rao, Z.Gong, H.

(2024) Nature 631: 409-414

  • DOI: https://doi.org/10.1038/s41586-024-07605-8
  • Primary Citation of Related Structures:  
    8J0S, 8J0T, 8J57, 8J58, 8JR0, 8JR1, 8KHF, 8KI3

  • PubMed Abstract: 

    Bedaquiline (BDQ), a first-in-class diarylquinoline anti-tuberculosis drug, and its analogue, TBAJ-587, prevent the growth and proliferation of Mycobacterium tuberculosis by inhibiting ATP synthase 1,2 . However, BDQ also inhibits human ATP synthase 3 . At present, how these compounds interact with either M. tuberculosis ATP synthase or human ATP synthase is unclear. Here we present cryogenic electron microscopy structures of M. tuberculosis ATP synthase with and without BDQ and TBAJ-587 bound, and human ATP synthase bound to BDQ. The two inhibitors interact with subunit a and the c-ring at the leading site, c-only sites and lagging site in M. tuberculosis ATP synthase, showing that BDQ and TBAJ-587 have similar modes of action. The quinolinyl and dimethylamino units of the compounds make extensive contacts with the protein. The structure of human ATP synthase in complex with BDQ reveals that the BDQ-binding site is similar to that observed for the leading site in M. tuberculosis ATP synthase, and that the quinolinyl unit also interacts extensively with the human enzyme. This study will improve researchers' understanding of the similarities and differences between human ATP synthase and M. tuberculosis ATP synthase in terms of the mode of BDQ binding, and will allow the rational design of novel diarylquinolines as anti-tuberculosis drugs.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c81Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpE
Membrane Entity: Yes 
UniProt
Find proteins for P9WPS1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPS1 
Go to UniProtKB:  P9WPS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPS1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aJ [auth a]250Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for P9WPV7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPV7 
Go to UniProtKB:  P9WPV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPV7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019
National Natural Science Foundation of China (NSFC)China32100976
National Natural Science Foundation of China (NSFC)China82222042

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references