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- PDB-24dk: Structural snapshots of F1-ATPase catalysis in drug resistant Aci... -

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Basic information

Entry
Database: PDB / ID: 24dk
TitleStructural snapshots of F1-ATPase catalysis in drug resistant Acinetobacter baumannii reveal novel therapeutic targets - Conformation 2a
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / ATP hydrolysis / F1-ATPase
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesAcinetobacter baumannii AB5075 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLe, K.C.M. / Gruber, G.
Funding support Singapore, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
e: ATP synthase epsilon chain
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
F: ATP synthase subunit beta
g: ATP synthase gamma chain
E: ATP synthase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,92718
Polymers364,0278
Non-polymers2,90010
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 4 types, 8 molecules eABCDFEg

#1: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14551.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: atpC, A7M90_08520, ABR2091_0173, ABUW_3731, APD06_01415, APD33_01490, AUO97_06420, B9W25_04440, B9X95_01230, C5U34_13725, CBE85_14435, CV954_019155, DOL94_02920, EA686_08570, EA722_10625, EJ062_ ...Gene: atpC, A7M90_08520, ABR2091_0173, ABUW_3731, APD06_01415, APD33_01490, AUO97_06420, B9W25_04440, B9X95_01230, C5U34_13725, CBE85_14435, CV954_019155, DOL94_02920, EA686_08570, EA722_10625, EJ062_16090, F2P40_12650, F4T83_15820, FJU42_13255, FPK63_14195, FPK81_12785, FPK87_05335, FQZ18_18385, G3N53_14500, GNY86_14290, GSE42_00725, IHV20_08040, IMO23_00750, J6E47_18610, JHZ39_002241, LV35_02739, MKP18_001736, MKP18_004274, MKP18_004275, P9867_000775, P9867_05900, SAMEA104305318_03328, SAMEA4394745_01411
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: V5VHG0
#2: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55452.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: atpA, ABR2091_0170, ABUW_3734, APD06_01400, APD33_01475, AUO97_06435, B9W25_04455, B9X95_01215, CBE85_14450, CV954_019170, DOL94_02905, EA686_04375, EA722_10610, EJ062_16075, F2P40_12665, FJU42_ ...Gene: atpA, ABR2091_0170, ABUW_3734, APD06_01400, APD33_01475, AUO97_06435, B9W25_04455, B9X95_01215, CBE85_14450, CV954_019170, DOL94_02905, EA686_04375, EA722_10610, EJ062_16075, F2P40_12665, FJU42_13270, FPK63_14180, FPK87_05320, FQZ18_18400, GNY86_14305, GSE42_00710, IHV20_08055, IMO23_00735, J6E47_18625, JHZ39_002238, LV35_02736, MKP18_001733, MKP18_004271, MKP18_004272, P9867_000760, P9867_05885, SAMEA104305318_03331
Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: V5VJ37, H+-transporting two-sector ATPase
#3: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50327.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: atpD, A7M90_08515, ABR2091_0172, ABUW_3732, APD06_01410, APD33_01485, AUO97_06425, B9W25_04445, B9X95_01225, C5U34_13730, CBE85_14440, CPI82_15305, CV954_019160, DOL94_02915, EA722_10620, EJ062_ ...Gene: atpD, A7M90_08515, ABR2091_0172, ABUW_3732, APD06_01410, APD33_01485, AUO97_06425, B9W25_04445, B9X95_01225, C5U34_13730, CBE85_14440, CPI82_15305, CV954_019160, DOL94_02915, EA722_10620, EJ062_16085, F2P40_12655, FJU42_13260, FPK63_14190, FPK87_05330, FQZ18_18390, G3N53_14495, GNY86_14295, GSE42_00720, IAG11_01885, IHV20_08045, IMO23_00745, J6E47_18615, JHZ39_002240, LV35_02738, MKP18_001735, MKP18_004273, MKP18_004274, P9867_000770, P9867_05895, SAMEA104305318_03329
Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: V5VHQ6, H+-transporting two-sector ATPase
#4: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 32135.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AB5075 (bacteria)
Gene: atpG, A7M90_08510, ABR2091_0171, ABUW_3733, APD06_01405, APD33_01480, AUO97_06430, B9W25_04450, B9X95_01220, C5U34_13735, CV954_019165, DOL94_02910, EA686_04380, EA722_10615, EJ062_16080, F2P40_ ...Gene: atpG, A7M90_08510, ABR2091_0171, ABUW_3733, APD06_01405, APD33_01480, AUO97_06430, B9W25_04450, B9X95_01220, C5U34_13735, CV954_019165, DOL94_02910, EA686_04380, EA722_10615, EJ062_16080, F2P40_12660, FJU42_13265, FPK63_14185, FPK87_05325, FQZ18_18395, G3N53_14490, GNY86_14300, GSE42_00715, IHV20_08050, J6E47_18620, JHZ39_002239, LV35_02737, MKP18_001734, MKP18_004272, MKP18_004273, P9867_000765, P9867_05890, SAMEA104305318_03330
Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: V5VHZ7

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Non-polymers , 3 types, 10 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acinetobacter baumannii F1-ATPase recombinant protein incubated with 12 uM MgADP + Pi
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.37 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41
Buffer solutionpH: 7.5 / Details: 50 mM Tris-HCl, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2150 mMNaClNaCl1
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 160000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.02 sec. / Electron dose: 68.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5094

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.6.0CTF correction
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 891625
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42341 / Symmetry type: POINT

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