7NKD

Mycobacterium smegmatis ATP synthase b-delta state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis.

Montgomery, M.G.Petri, J.Spikes, T.E.Walker, J.E.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2111899118
  • Primary Citation of Related Structures:  
    7NJK, 7NJL, 7NJM, 7NJN, 7NJO, 7NJP, 7NJQ, 7NJR, 7NJS, 7NJT, 7NJU, 7NJV, 7NJW, 7NJX, 7NJY, 7NK7, 7NK9, 7NKB, 7NKD, 7NKH, 7NKJ, 7NKK, 7NKL, 7NKN, 7NKP, 7NKQ, 7NL9

  • PubMed Abstract: 

    The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from Mycobacterium smegmatis This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a "fail-safe" mechanism involving the b'-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated "fail-safe" mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.


  • Organizational Affiliation

    The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
548Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpAMSMEG_4938MSMEI_4811
EC: 7.1.2.2
UniProt
Find proteins for A0R202 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R202
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 beta
D, E, F
475Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpDMSMEG_4936MSMEI_4809
EC: 7.1.2.2
UniProt
Find proteins for A0R200 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R200
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit b-deltaG [auth d]445Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpFHatpFatpHMSMEG_4939MSMEI_4812
UniProt
Find proteins for A0R203 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R203
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bH [auth b]180Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: atpFMSMEG_4940MSMEI_4813
UniProt
Find proteins for A0R204 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R204
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M009858/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/8

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection