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- EMDB-60117: Cryo-EM reveals transition states of the Acinetobacter baumannii ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60117
TitleCryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 1
Map data
Sample
  • Complex: Acinetobacter baumannii F1-ATPase recombinant protein with truncation mutation at subunit epsilon CTD, 134-139
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
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 ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / hydrolase activity / ATP hydrolysis activity / 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 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 / 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 subunit alpha / ATP synthase gamma chain / ATP synthase epsilon chain / ATP synthase subunit beta
Similarity search - Component
Biological speciesAcinetobacter baumannii AB5075 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLe KCM / Wong CF / Gruber G
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)RG20/22 Singapore
CitationJournal: FASEB J / Year: 2024
Title: Cryo-EM reveals transition states of the Acinetobacter baumannii F-ATPase rotary subunits γ and ε, unveiling novel compound targets.
Authors: Khoa Cong Minh Le / Chui Fann Wong / Volker Müller / Gerhard Grüber /
Abstract: Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional FF-ATP synthase. While synthesizing ATP, it regulates ATP cleavage by ...Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional FF-ATP synthase. While synthesizing ATP, it regulates ATP cleavage by its inhibitory ε subunit to prevent wasteful ATP consumption. We determined cryo-electron microscopy structures of the ATPase active A. baumannii F-αßγε mutant in four distinct conformational states, revealing four transition states and structural transformation of the ε's C-terminal domain, forming the switch of an ATP hydrolysis off- and an ATP synthesis on-state based. These alterations go in concert with altered motions and interactions in the catalytic- and rotary subunits of this engine. These A. baumannii interacting sites provide novel pathogen-specific targets for inhibitors, with the aim of ATP depletion and/or ATP synthesis and growth inhibition. Furthermore, the presented diversity to other bacterial F-ATP synthases extends the view of structural elements regulating such a catalyst.
History
DepositionMay 12, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60117.png

Downloads & links

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Map

FileDownload / File: emd_60117.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 343.2 Å		0.86 Å/pix.
x 400 pix.
= 343.2 Å		0.86 Å/pix.
x 400 pix.
= 343.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.078
Minimum - Maximum-0.28069457 - 0.5751648
Average (Standard dev.)0.00010834315 (±0.016810495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 343.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60117_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60117_half_map_1.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Acinetobacter baumannii F1-ATPase recombinant protein with trunca...

EntireName: Acinetobacter baumannii F1-ATPase recombinant protein with truncation mutation at subunit epsilon CTD, 134-139
Components
  • Complex: Acinetobacter baumannii F1-ATPase recombinant protein with truncation mutation at subunit epsilon CTD, 134-139
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Acinetobacter baumannii F1-ATPase recombinant protein with trunca...

SupramoleculeName: Acinetobacter baumannii F1-ATPase recombinant protein with truncation mutation at subunit epsilon CTD, 134-139
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 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: 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 #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: 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 #3: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 3
Details: Subunit epsilon with truncated C-terminus domain, deletion I134-Q139
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 13.83884 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MATMQCDVVS VKESIYSGAV TMLIAKGAGG ELGILPGHAP LVTLLQPGPI RVLLENGTEE IVYVSGGVLE VQPHVVTVLA DTAIRADNL DEAAILEARK NAEQLLANQK SDLDSAAALA ALAETAAQLE TIRK

UniProtKB: ATP synthase epsilon chain

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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: 1 / 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 #8: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration1.5 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8635 / 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: 829861
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 47078
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7yry


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model is from the CryoEM structure of AbF1-ATPase Wild Type form.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8zi0:
Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits gamma and epsilon and novel compound targets - Conformation 1

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