8J0S

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with bedaquiline(BDQ)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aA [auth a]250Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for P9WPV7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WPV7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaB [auth A],
C [auth B],
D [auth C]
549Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpARv1308MTCY373.28
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P9WPU7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WPU7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaE [auth D],
F [auth E],
G [auth F]
486Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpDRv1310MTCY373.30
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P9WPU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WPU5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chainH [auth G]305Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpGRv1309MTCY373.29
Membrane Entity: Yes 
UniProt
Find proteins for P9WPU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainI [auth H]121Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpCRv1311MTCY373.31
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c81Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpE
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bS [auth b]171Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpF
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional fusion proteinT [auth d]446Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpH
Membrane Entity: Yes 
UniProt
Find proteins for P9WPV3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BQ1
Query on BQ1

Download Ideal Coordinates CCD File 
EA [auth 1]
FA [auth 4]
GA [auth 5]
HA [auth 6]
IA [auth 7]
EA [auth 1],
FA [auth 4],
GA [auth 5],
HA [auth 6],
IA [auth 7],
JA [auth 8],
KA [auth 9]
Bedaquiline
C32 H31 Br N2 O2
QUIJNHUBAXPXFS-XLJNKUFUSA-N
ATP
Query on ATP

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U [auth A],
W [auth B],
Y [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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AA [auth D],
CA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

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BA [auth D],
DA [auth F],
V [auth A],
X [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references