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- EMDB-49999: Pseudomonas aeruginosa ATPase State1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49999
TitlePseudomonas aeruginosa ATPase State1
Map dataPseudomonas aeruginosa ATPase State1
Sample
  • Complex: Pseudomonas aeruginosa ATPase
    • Protein or peptide: x 6 types
  • Ligand: x 5 types
KeywordsATPase / energy / ELECTRON TRANSPORT
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / : / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit b
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsStewart AG / Sobti M
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Distinct Structural Features of Pseudomonas aeruginosa ATP Synthase Revealed by Cryo Electron Microscopy
Authors: Sobti M / Stewart AG
History
DepositionApr 3, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49999.png

Downloads & links

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Map

FileDownload / File: emd_49999.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudomonas aeruginosa ATPase State1
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: 0.06
Minimum - Maximum-0.24262409 - 0.7164419
Average (Standard dev.)0.0018856126 (±0.014982446)
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_49999_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_49999_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 alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit b
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Pseudomonas aeruginosa ATPase

SupramoleculeName: Pseudomonas aeruginosa ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 55.264785 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQQLNPSEIS EIIKGRIEKL DVASQARNEG TIVSVSDGIV RIYGLADVMY GEMIEFPGGV YGMALNLEQD SVGAVVLGEY QGLAEGMNA KCTGRILEVP VGPELLGRVV DALGNPIDGK GPIDAKATDA VEKVAPGVIW RKSVDQPVQT GYKSVDAMIP V GRGQRELI ...String:
MQQLNPSEIS EIIKGRIEKL DVASQARNEG TIVSVSDGIV RIYGLADVMY GEMIEFPGGV YGMALNLEQD SVGAVVLGEY QGLAEGMNA KCTGRILEVP VGPELLGRVV DALGNPIDGK GPIDAKATDA VEKVAPGVIW RKSVDQPVQT GYKSVDAMIP V GRGQRELI IGDRQIGKTA LAVDAIINQK DSGIKCVYVA IGQKQSTIAN VVRKLEENGA LANTIVVAAS ASESAALQYL AP YSGCTMG EYFRDRGEDA LIVYDDLSKQ AVAYRQISLL LRRPPGREAY PGDVFYLHSR LLERASRVSE EYVEKFTNGA VTG KTGSLT ALPIIETQAG DVSAFVPTNV ISITDGQIFL ESAMFNSGIR PAVNAGISVS RVGGAAQTKI IKKLSGGIRT ALAQ YRELA AFAQFASDLD EATRKQLEHG QRVTELMKQK QYAPMSIAEM SLSLYAAERG FLQDVEIAKV GSFEQALISY FQREH AALL AKINEKGDFN DEIDAGIKAG IEKFKATQT

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 50.380129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG RIVQIIGAVI DVEFPRDAVP SIYEALKVQG VETTLEVQQQ LGDGVVRSIA MGSTEGLKRG LNVDSTGAAI SVPVGKATL GRIMDVLGNP IDEAGPIGEE ERWGIHREAP SYADQAGGNE LLETGIKVID LVCPFAKGGK VGLFGGAGVG K TVNMMELI ...String:
MHHHHHHSSG RIVQIIGAVI DVEFPRDAVP SIYEALKVQG VETTLEVQQQ LGDGVVRSIA MGSTEGLKRG LNVDSTGAAI SVPVGKATL GRIMDVLGNP IDEAGPIGEE ERWGIHREAP SYADQAGGNE LLETGIKVID LVCPFAKGGK VGLFGGAGVG K TVNMMELI RNIAIEHSGY SVFAGVGERT REGNDFYHEM KDSNVLDKVA LVYGQMNEPP GNRLRVALTG LTMAEKFRDE GR DVLLFID NIYRYTLAGT EVSALLGRMP SAVGYQPTLA EEMGVLQERI TSTKKGSITS IQAVYVPADD LTDPSPATTF AHL DATVVL SRDIASLGIY PAVDPLDSTS RQLDPLVIGQ DHYDTARGVQ YVLQRYKELK DIIAILGMDE LSEADKLLVA RARK IQRFL SQPFFVAEVF TGSPGKYVSL KDTIAGFKGI LNGDYDHLPE QAFYMVGGIE EAVEKAKKL

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 31.593328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGAKEIRSK IASIKSTQKI TNAMEKVAVS KMRKAQMRMA AGRPYAERIR QVIGHLANAN PEYRHPFMVE REVKRVGYIV VSSDRGLCG GLNINLFKSL VKDMSGYREQ GAEIDLCVIG SKGASFFRSF GGNVVAAISH LGEEPSINDL IGSVKVMLDA Y LEGRIDRL ...String:
MAGAKEIRSK IASIKSTQKI TNAMEKVAVS KMRKAQMRMA AGRPYAERIR QVIGHLANAN PEYRHPFMVE REVKRVGYIV VSSDRGLCG GLNINLFKSL VKDMSGYREQ GAEIDLCVIG SKGASFFRSF GGNVVAAISH LGEEPSINDL IGSVKVMLDA Y LEGRIDRL FVVSNKFVNT MTQKPTVEQL IPLVADDDQE LKHHWDYLYE PDAKSLLDGL LVRYVESQVY QAVVENNACE QA ARMIAMK NATDNAGELI SDLQLIYNKA RQAAITQEIS EIVGGAAAV

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 14.741866 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITVHCDIV SAEAEIFSGL VEMVIAHGAL GDLGIAPGHA PLITDLKPGP IRLVKQGGEQ EVYYISGGFL EVQPNMVKVL ADTVVRAGD LDEAAAQEAL KAAEKALQGK GAEFDYSAAA ARLAEAAAQL RTVQQLRKKF GG

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.28398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAELTTLARP YAKAAFEYAQ AHQQLADWSA ALGVLAAVSQ DDTVRQLLKE PQLTSSAKAQ SLIDVCGDKL NAPAQNFVRT VAENKRLEL LPTIAEMYEQ LKAEQEKSVE VEVTSAFTLS KEQQDKLAKA LSARLSREVR LHASEDASLI GGVIIRAGDL V IDGSVRGK LAKLAEALKS

UniProtKB: ATP synthase subunit delta

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Macromolecule #6: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 6 / 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 #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #10: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 1345 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219554
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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