9O1J | pdb_00009o1j

Pseudomonas aeruginosa ATPase State3 F1Fo focused


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Distinct structural features of Pseudomonas aeruginosa ATP synthase revealed by cryo-electron microscopy.

Sobti, M.Gunn, A.P.Brown, S.H.J.Zavan, L.Fraunfelter, V.M.Wolfe, A.L.McDevitt, C.A.Steed, P.R.Stewart, A.G.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-67100-0
  • Primary Citation of Related Structures:  
    9O19, 9O1A, 9O1B, 9O1C, 9O1D, 9O1E, 9O1F, 9O1G, 9O1H, 9O1J, 9O1K

  • PubMed Abstract: 

    F 1 F o ATP synthase is the ubiquitous enzyme that synthesizes cellular ATP by coupling proton-motive force with rotational catalysis. Structural differences between prokaryotic and eukaryotic ATP synthases offer potential targets for antimicrobial development. Here, we present the 2.0-2.4 Å resolution cryo-electron microscopy structures of the ATP synthase from Pseudomonas aeruginosa, an opportunistic bacterial pathogen capable of causing serious infections in humans. Our structures identify two distinctive features of this species' enzyme: a distinct binding site for the inhibitory ε subunit, and a coordinated metal ion capping the cytoplasmic proton channel. Lower-resolution maps of the enzyme following incubation with MgATP showed conformational rearrangements of the ε subunit during activation. Visualization of bound water molecules in the periplasmic half-channel supports a Grotthuss proton-transfer mechanism. Focused classification of the F o motor resolves distinct ~11° sub-steps in the c-ring, corresponding to protonation and deprotonation events. Functional analyses show that modifications to either the ε subunit or the metal binding site influence ATP synthesis and hydrolysis. Mass spectrometry analyses suggests that the physiological metal within the complex is zinc. Collectively, these findings define structural features of P. aeruginosa ATP synthase that could serve as targets for antimicrobial therapeutics.


  • Organizational Affiliation
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
514Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpAPSPA7_6358
EC: 7.1.2.2
UniProt
Find proteins for A6VF34 (Pseudomonas paraeruginosa (strain DSM 24068 / PA7))
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UniProt GroupA6VF34
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
464Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpDPSPA7_6356
EC: 7.1.2.2
UniProt
Find proteins for A6VF32 (Pseudomonas paraeruginosa (strain DSM 24068 / PA7))
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UniProt GroupA6VF32
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain286Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpGPSPA7_6357
UniProt
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UniProt GroupA6VF33
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain141Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpCPSPA7_6355
UniProt
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UniProt GroupA6VF31
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c85Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpEPSPA7_6361
UniProt
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UniProt GroupA6VF37
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaS [auth W]178Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpHPSPA7_6359
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bT [auth X],
U [auth Y]
156Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpFPA14_73290
UniProt
Find proteins for Q02DF0 (Pseudomonas aeruginosa (strain UCBPP-PA14))
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UniProt GroupQ02DF0
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aV [auth a]289Pseudomonas aeruginosaMutation(s): 0 
Gene Names: atpBPSPA7_6362
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 
AA [auth C],
W [auth A],
Y [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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

Download Ideal Coordinates CCD File 
BA [auth C],
DA [auth D],
FA [auth E],
X [auth A],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references