8JR0 | pdb_00008jr0

Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with TBAJ-587


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 558.63 kDa 
  • Atom Count: 37,460 
  • Modeled Residue Count: 4,889 
  • Deposited Residue Count: 5,127 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, 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))
Explore P9WPU7 
Go to UniProtKB:  P9WPU7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPU7
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, 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))
Explore P9WPU5 
Go to UniProtKB:  P9WPU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPU5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chain305Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpGRv1309MTCY373.29
Membrane Entity: Yes 
UniProt
Find proteins for P9WPU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPU9 
Go to UniProtKB:  P9WPU9
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UniProt GroupP9WPU9
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain121Mycobacterium tuberculosisMutation(s): 0 
Gene Names: atpCRv1311MTCY373.31
Membrane Entity: Yes 
UniProt
Find proteins for P9WPV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPV1 
Go to UniProtKB:  P9WPV1
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Reference Sequence
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Entity ID: 5
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))
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UniProt GroupP9WPS1
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit aR [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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Reference Sequence
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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
Find proteins for P9WPV5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Reference Sequence
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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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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UTI

Query on UTI



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]
(1~{S},2~{S})-1-(6-bromanyl-2-methoxy-quinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2-fluoranyl-3-methoxy-phenyl)butan-2-ol
C30 H33 Br F N3 O5
JJEGOJPMKLRSPJ-POURPWNDSA-N
ATP

Query on ATP



Download:Ideal Coordinates CCD File
U [auth A],
W [auth B],
Y [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
AA [auth D],
CA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
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: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.2: 2025-06-18
    Changes: Data collection, Structure summary