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- EMDB-70010: Pseudomonas aeruginosa ATPase State3 Fo focused -

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Basic information

Entry
Database: EMDB / ID: EMD-70010
TitlePseudomonas aeruginosa ATPase State3 Fo focused
Map dataPseudomonas aeruginosa ATPase State3 Fo focused
Sample
  • Complex: Pseudomonas aeruginosa ATPase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: ATP synthase subunit a
KeywordsATPase / energy / ELECTRON TRANSPORT
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily ...ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit c / ATP synthase subunit a / ATP synthase subunit b
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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
DepositionApr 3, 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_70010.png

Downloads & links

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Map

FileDownload / File: emd_70010.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa ATPase State3 Fo focused
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. 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: 0.04
Minimum - Maximum-0.10000211 - 0.24775156
Average (Standard dev.)0.0003184356 (±0.005904184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_70010_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70010_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

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
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit b
  • Protein or peptide: ATP synthase subunit a

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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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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 8.61138 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
METVVGLTAI AVALLIGLGA LGTAIGFGLL GGKFLEGAAR QPEMVPMLQV KMFIVAGLLD AVTMIGVGIA LFFTFANPFV GQIAG

UniProtKB: ATP synthase subunit c

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Macromolecule #2: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 16.978346 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNINATLIGQ SVAFFIFVLF CMKFVWPPVI AALQERQKKI ADGLDAANRA ARDLELAHEK AGQQLREAKA QAAEIVEQAK KRANQIVDE ARDQARTEGE RLKAQAQAEI EQELNSVKDA LRAQVGALAV TGAEKILGAS IDANAHEQLV SKLAAEI

UniProtKB: ATP synthase subunit b

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Macromolecule #3: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 31.944635 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAETASGYI QHHLQNLTFG RLPNGDWGFA HTAEQAKEMG FWAFHVDTLG WSVLLGVVFL FIFRLAAKKA TSGQPGGLQN FVEVMVEFV DTSVKDTFHG RNPLIAPLAL TVFVWIFLLN LIDLVPVDYL PMLAAKITGD EHLFFRAVAT TDPNATLGLS I SVFALIVF ...String:
MAAETASGYI QHHLQNLTFG RLPNGDWGFA HTAEQAKEMG FWAFHVDTLG WSVLLGVVFL FIFRLAAKKA TSGQPGGLQN FVEVMVEFV DTSVKDTFHG RNPLIAPLAL TVFVWIFLLN LIDLVPVDYL PMLAAKITGD EHLFFRAVAT TDPNATLGLS I SVFALIVF YSIKVKGIGG FLGELTLHPF SSKNIVVQIL LIPVNFLLEF VTLIAKPVSL ALRLFGNMYA GELIFILIAV MF GSGMFLL SALGVALNWA WAVFHILIIT LQAFIFMMLT IVYLSMAHED NH

UniProtKB: ATP synthase subunit a

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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: 65.0 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: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56137
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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