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- EMDB-69447: Structural snapshots of F1-ATPase catalysis in drug resistant Aci... -

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Basic information

Entry
Database: EMDB / ID: EMD-69447
TitleStructural snapshots of F1-ATPase catalysis in drug resistant Acinetobacter baumannii reveal novel therapeutic targets - Conformation 2a
Map data
Sample
  • Complex: Acinetobacter baumannii F1-ATPase recombinant protein incubated with 12 uM MgADP + Pi
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP hydrolysis / F1-ATPase / HYDROLASE
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, gamma subunit ...ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / 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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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
Similarity search - Component
Biological speciesAcinetobacter baumannii AB5075 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLe KCM / Gruber G
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF- CRP27-2021-0002 Singapore
CitationJournal: FASEB J / Year: 2026
Title: Structural Snapshots of F-ATPase Catalysis in Drug Resistant Acinetobacter baumannii Reveal Novel Therapeutic Targets.
Authors: Khoa C M Le / Jan K Marzinek / Vikneswaran Mathiyazakan / Peter J Bond / Gerhard Grüber /
Abstract: Gram-negative Acinetobacter baumannii, one of the most critical priority pathogens, has developed multiple defense mechanisms, including upregulation of drug efflux pumps powered by the proton-motive ...Gram-negative Acinetobacter baumannii, one of the most critical priority pathogens, has developed multiple defense mechanisms, including upregulation of drug efflux pumps powered by the proton-motive force (pmf) or ATP. As a nonfermenting bacterium, it relies on oxidative phosphorylation, in which the F-ATP synthase, composed of an F-ATPase (α:β:γ:ε) and F-domain (a:b:c), synthesizes ATP, the cell's currency of life. Here, we present cryo-electron microscopy structures of the F-ATPase captured during ATP synthesis, revealing concerted conformational changes within the α:β-catalytic head that trigger structural transitions of subunit ε and twisting of the γ:ε central stalk, coupled with spontaneous ATP formation. Molecular dynamics simulations validate and expand the ensemble of structural rearrangements underlying the rotary mechanism. The resolved intermediate states of the ε subunit reveal its role as a molecular gear, regulating ATP synthesis while simultaneously inhibiting ATP hydrolysis, essential for the pathogen to prevent wastage of ATP. These structural snapshots identify novel therapeutic targets and pave the way for rational design of selective inhibitors.
History
DepositionFeb 28, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69447.png

Downloads & links

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Map

FileDownload / File: emd_69447.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 350 pix.
= 300.3 Å		0.86 Å/pix.
x 350 pix.
= 300.3 Å		0.86 Å/pix.
x 350 pix.
= 300.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0626
Minimum - Maximum-0.2863224 - 0.67968965
Average (Standard dev.)-0.00026699336 (±0.022340149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 300.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69447_msk_1.map
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Half map: #2

Fileemd_69447_half_map_1.map
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Half map: #1

Fileemd_69447_half_map_2.map
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Sample components

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Entire : Acinetobacter baumannii F1-ATPase recombinant protein incubated w...

EntireName: Acinetobacter baumannii F1-ATPase recombinant protein incubated with 12 uM MgADP + Pi
Components
  • Complex: Acinetobacter baumannii F1-ATPase recombinant protein incubated with 12 uM MgADP + Pi
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Acinetobacter baumannii F1-ATPase recombinant protein incubated w...

SupramoleculeName: Acinetobacter baumannii F1-ATPase recombinant protein incubated with 12 uM MgADP + Pi
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 14.551682 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MATMQCDVVS VKESIYSGAV TMLIAKGAGG ELGILPGHAP LVTLLQPGPI RVLLENGTEE IVYVSGGVLE VQPHVVTVLA DTAIRADNL DEAAILEARK NAEQLLANQK SDLDSAAALA ALAETAAQLE TIRKIKNRAQ

UniProtKB: ATP synthase epsilon chain

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Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 55.452906 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MQQLNPSEIS ALIKQRIGDL DTSATAKNEG TIVMVSDGIV RIHGLADAMY GEMIEFDGGL FGMALNLEQD SVGAVVLGNY LSLQEGQKA RCTGRVLEVP VGPELLGRVV DALGNPIDGK GPIDAKLTDA VEKVAPGVIW RQSVDQPVQT GYKSVDTMIP V GRGQRELI ...String:
MQQLNPSEIS ALIKQRIGDL DTSATAKNEG TIVMVSDGIV RIHGLADAMY GEMIEFDGGL FGMALNLEQD SVGAVVLGNY LSLQEGQKA RCTGRVLEVP VGPELLGRVV DALGNPIDGK GPIDAKLTDA VEKVAPGVIW RQSVDQPVQT GYKSVDTMIP V GRGQRELI IGDRQTGKTA MAIDAIIAQK NSGIKCVYVA IGQKQSTIAN VVRKLEETGA MAYTTVVAAA AADPAAMQYL AP YSGCTMG EYFRDRGEDA LIIYDDLSKQ AVAYRQISLL LRRPPGREAY PGDVFYLHSR LLERASRVSA EYVEKFTNGA VTG KTGSLT ALPIIETQAG DVSAFVPTNV ISITDGQIFL ETSLFNAGIR PAVNAGISVS RVGGSAQTKI IKKLSGGIRT ALAQ YRELA AFAQFASDLD EATRKQLEHG QRVTELMKQK QYAPYSIADQ AVSVYASNEG YMADVEVKKI VDFDAALIAY FRSEY APLM KQIDETGDYN KDIEAAIKAG IESFKATQTY

UniProtKB: ATP synthase subunit alpha

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Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 50.32718 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSGRIIQII GAVIDVEFER TSVPKIYDAL QVDGTETTLE VQQQLGDGVV RTIAMGSTEG LKRGLTVTST NAPISVPVGT ATLGRIMDV LGRPIDEAGP VATEERLPIH RQAPSYAEQA ASTDLLETGI KVIDLLCPFA KGGKVGLFGG AGVGKTVNMM E LINNIAKA ...String:
MSSGRIIQII GAVIDVEFER TSVPKIYDAL QVDGTETTLE VQQQLGDGVV RTIAMGSTEG LKRGLTVTST NAPISVPVGT ATLGRIMDV LGRPIDEAGP VATEERLPIH RQAPSYAEQA ASTDLLETGI KVIDLLCPFA KGGKVGLFGG AGVGKTVNMM E LINNIAKA HSGLSVFAGV GERTREGNDF YHEMKDSNVL DKVAMVYGQM NEPPGNRLRV ALTGLTMAEY FRDEKDENGK GR DVLLFVD NIYRYTLAGT EVSALLGRMP SAVGYQPTLA EEMGVLQERI TSTKSGSITS IQAVYVPADD LTDPSPATTF AHL DATVVL SRDIASSGIY PAIDPLDSTS RQLDPLVVGQ EHYEIARAVQ NVLQRYKELK DIIAILGMDE LAEEDKLVVY RARK IQRFF SQPFHVAEVF TGAPGKLVPL KETIRGFKGL LAGEYDHIPE QAFYMVGGID EVIAKAEKL

UniProtKB: ATP synthase subunit beta

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Macromolecule #4: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 32.135037 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MANLKEIRAK VASIKSTQKI TRAMQMVAAS KMRRAQERMA QGRPYADNMR RVIAHLVQAN PEYKHRYMVD RPVKRVGYII VSSDRGLAG GLNINLFKKV VQHVKAQQEQ SIEVQFALIG QKAVSFFKNY GGKVLGATTQ IGDAPSLEQL TGSVQVMLDA F DKGELDRI ...String:
MANLKEIRAK VASIKSTQKI TRAMQMVAAS KMRRAQERMA QGRPYADNMR RVIAHLVQAN PEYKHRYMVD RPVKRVGYII VSSDRGLAG GLNINLFKKV VQHVKAQQEQ SIEVQFALIG QKAVSFFKNY GGKVLGATTQ IGDAPSLEQL TGSVQVMLDA F DKGELDRI YLVSNGFVNA MTQKPKVEQL VPLAPAEEGD DLNRTYGWDY IYEPEAEELL NGLLVRYIES MVYQGVIENV AC EQSARMV AMKAATDNAG QLIKDLQLIY NKLRQAAITQ EISEIVGGAA AV

UniProtKB: ATP synthase gamma chain

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
150.0 mMNaClNaCl

Details: 50 mM Tris-HCl, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5094 / Average exposure time: 6.02 sec. / Average electron dose: 68.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 160000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 891625
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 42341
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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