7Y5B

Cryo-EM structure of F-ATP synthase from Mycolicibacterium smegmatis (rotational state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors.

Wong, C.F.Saw, W.G.Basak, S.Sano, M.Ueno, H.Kerk, H.W.Litty, D.Ragunathan, P.Dick, T.Muller, V.Noji, H.Gruber, G.

(2022) Antimicrob Agents Chemother 66: e0105622-e0105622

  • DOI: https://doi.org/10.1128/aac.01056-22
  • Primary Citation of Related Structures:  
    7Y5A, 7Y5B, 7Y5C, 7Y5D

  • PubMed Abstract: 

    The F 1 F O -ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F 1 -ATPase and the F 1 F O -ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors.


  • Organizational Affiliation

    School of Biological Sciences, Nanyang Technological Universitygrid.59025.3b, Singapore, Singapore.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B
548Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpAMSMEG_4938MSMEI_4811
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R202
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha548Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpAMSMEG_4938MSMEI_4811
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R202
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
481Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpDMSMEG_4936MSMEI_4809
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0R200 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R200
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain307Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpGMSMEG_4937MSMEI_4810
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain121Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpCMSMEG_4935MSMEI_4808
Membrane Entity: Yes 
UniProt
Find proteins for A0R1Z9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aI [auth a]252Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpBMSMEG_4942
Membrane Entity: Yes 
UniProt
Find proteins for A0R206 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bJ [auth b]170Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpFMSMEG_4940MSMEI_4813
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit b-deltaK [auth d]445Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpFHatpFatpHMSMEG_4939MSMEI_4812
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c86Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: atpEMSMEG_4941
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
BA [auth E],
DA [auth F],
U [auth A],
W [auth B],
Y [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth E],
EA [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: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-CRP18-2017-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references
  • Version 1.3: 2023-01-04
    Changes: Database references
  • Version 1.4: 2023-01-11
    Changes: Database references
  • Version 1.5: 2024-07-03
    Changes: Data collection