9O1G | pdb_00009o1g

Pseudomonas aeruginosa ATPase State2b Fo focused

• PDB DOI: https://doi.org/10.2210/pdb9O1G/pdb
• EM Map EMD-70006: EMDB EMDataResource

• Classification: ELECTRON TRANSPORT
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-03 Released: 2025-12-10 
• Deposition Author(s): Stewart, A.G., Sobti, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 

• PubMed: 41366214 
• 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.

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Organizational Affiliation: 
• Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia.
School of Science, Molecular Horizons, and the Australian Research Council Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia.
Department of Chemistry and Biochemistry, University of North Carolina Asheville, Asheville, NC, USA.
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia. [e-mail].
School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A10B2C1 

Local Symmetry: Cyclic - C10  (Explore in 3D)
Local Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 152.08 kDa 
• Atom Count: 8,915 
• Modeled Residue Count: 1,210 
• Deposited Residue Count: 1,451 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit c	A [auth I], B [auth J], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S]	85	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: atpE, PSPA7_6361
UniProt
Find proteins for A6VF37 (Pseudomonas paraeruginosa (strain DSM 24068 / PA7)) Explore A6VF37  Go to UniProtKB:  A6VF37

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	K [auth X], L [auth Y]	156	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: atpF, PA14_73290
UniProt
Find proteins for Q02DF0 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02DF0  Go to UniProtKB:  Q02DF0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	M [auth a]	289	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: atpB, PSPA7_6362
UniProt
Find proteins for A6VF38 (Pseudomonas paraeruginosa (strain DSM 24068 / PA7)) Explore A6VF38  Go to UniProtKB:  A6VF38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	N [auth a]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Stewart, A.G., Sobti, M.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

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