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- EMDB-71967: Pseudomonas aeruginosa ATPase State2 with 10mM MgATP "Up" -

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Basic information

Entry
Database: EMDB / ID: EMD-71967
TitlePseudomonas aeruginosa ATPase State2 with 10mM MgATP "Up"
Map dataPseudomonas aeruginosa ATPase State2 with 10mM MgATP "Up"
Sample
  • Complex: Pseudomonas aeruginosa ATPase
KeywordsATPase / energy / ELECTRON TRANSPORT
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsStewart AG / Sobti M
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Nat Commun / Year: 2025
Title: Distinct structural features of Pseudomonas aeruginosa ATP synthase revealed by cryo-electron microscopy.
Authors: Meghna Sobti / Adam P Gunn / Simon H J Brown / Lauren Zavan / Vesper M Fraunfelter / Amanda L Wolfe / Christopher A McDevitt / P Ryan Steed / Alastair G Stewart /
Abstract: FF 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 ...FF 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 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.
History
DepositionAug 5, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71967.png

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Map

FileDownload / File: emd_71967.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa ATPase State2 with 10mM MgATP "Up"
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 Å		0.83 Å/pix.
x 448 pix.
= 371.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.40500176 - 0.7004109
Average (Standard dev.)0.00057932216 (±0.02158684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 371.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71967_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71967_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas aeruginosa ATPase

EntireName: Pseudomonas aeruginosa ATPase
Components
  • Complex: Pseudomonas aeruginosa ATPase

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Supramolecule #1: Pseudomonas aeruginosa ATPase

SupramoleculeName: Pseudomonas aeruginosa ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45727
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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