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- EMDB-34066: F1-ATPase of Acinetobacter baumannii -

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Basic information

Entry
Database: EMDB / ID: EMD-34066
TitleF1-ATPase of Acinetobacter baumannii
Map dataComposite map of consensus maps 1 and 2
Sample
  • Complex: F1-ATPase of Acinetobacter baumannii
    • 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
KeywordsF1-ATPase / Acinetobacter baumannii / 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 / 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 subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria) / Acinetobacter baumannii AB5075 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSaw W-G / Grueber G
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: FASEB J / Year: 2023
Title: Atomic insights of an up and down conformation of the Acinetobacter baumannii F -ATPase subunit ε and deciphering the residues critical for ATP hydrolysis inhibition and ATP synthesis.
Authors: Wuan-Geok Saw / Khoa Cong Minh Le / Joon Shin / Jes Hui Min Kwek / Chui Fann Wong / Priya Ragunathan / Tuck Choy Fong / Volker Müller / Gerhard Grüber /
Abstract: The Acinetobacter baumannii F F -ATP synthase (α :β :γ:δ:ε:a:b :c ), which is essential for this strictly respiratory opportunistic human pathogen, is incapable of ATP-driven proton ...The Acinetobacter baumannii F F -ATP synthase (α :β :γ:δ:ε:a:b :c ), which is essential for this strictly respiratory opportunistic human pathogen, is incapable of ATP-driven proton translocation due to its latent ATPase activity. Here, we generated and purified the first recombinant A. baumannii F -ATPase (AbF -ATPase) composed of subunits α :β :γ:ε, showing latent ATP hydrolysis. A 3.0 Å cryo-electron microscopy structure visualizes the architecture and regulatory element of this enzyme, in which the C-terminal domain of subunit ε (Abε) is present in an extended position. An ε-free AbF -ɑβγ complex generated showed a 21.5-fold ATP hydrolysis increase, demonstrating that Abε is the major regulator of AbF -ATPase's latent ATP hydrolysis. The recombinant system enabled mutational studies of single amino acid substitutions within Abε or its interacting subunits β and γ, respectively, as well as C-terminal truncated mutants of Abε, providing a detailed picture of Abε's main element for the self-inhibition mechanism of ATP hydrolysis. Using a heterologous expression system, the importance of Abε's C-terminus in ATP synthesis of inverted membrane vesicles, including AbF F -ATP synthases, has been explored. In addition, we are presenting the first NMR solution structure of the compact form of Abε, revealing interaction of its N-terminal β-barrel and C-terminal ɑ-hairpin domain. A double mutant of Abε highlights critical residues for Abε's domain-domain formation which is important also for AbF -ATPase's stability. Abε does not bind MgATP, which is described to regulate the up and down movements in other bacterial counterparts. The data are compared to regulatory elements of F -ATPases in bacteria, chloroplasts, and mitochondria to prevent wasting of ATP.
History
DepositionAug 11, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34066.png

Downloads & links

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Map

FileDownload / File: emd_34066.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of consensus maps 1 and 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 348 pix.
= 298.723 Å		0.86 Å/pix.
x 348 pix.
= 298.723 Å		0.86 Å/pix.
x 348 pix.
= 298.723 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8584 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.013486429 - 0.037063792
Average (Standard dev.)0.00008525959 (±0.0010256354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 298.7232 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34066_msk_1.map
Projections & Slices
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Mask #2

Fileemd_34066_msk_2.map
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Additional map: Consensus map 1

Fileemd_34066_additional_1.map
AnnotationConsensus map 1
Projections & Slices
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Additional map: Consensus map 2

Fileemd_34066_additional_2.map
AnnotationConsensus map 2
Projections & Slices
AxesZYX

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Additional map: Consensus map 2 half map 1

Fileemd_34066_additional_3.map
AnnotationConsensus map 2 half map 1
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Additional map: Consensus map 2 half map 2

Fileemd_34066_additional_4.map
AnnotationConsensus map 2 half map 2
Projections & Slices
AxesZYX

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Histogram

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Half map: Consensus map 1 half map 2

Fileemd_34066_half_map_1.map
AnnotationConsensus map 1 half map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Consensus map 1 half map 1

Fileemd_34066_half_map_2.map
AnnotationConsensus map 1 half map 1
Projections & Slices
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Sample components

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Entire : F1-ATPase of Acinetobacter baumannii

EntireName: F1-ATPase of Acinetobacter baumannii
Components
  • Complex: F1-ATPase of Acinetobacter baumannii
    • 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: F1-ATPase of Acinetobacter baumannii

SupramoleculeName: F1-ATPase of Acinetobacter baumannii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: AB5075
Molecular weightTheoretical: 363.5 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)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
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
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Molecular weightTheoretical: 51.156055 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHSSG RIIQIIGAVI DVEFERTSVP KIYDALQVDG TETTLEVQQQ LGDGVVRTIA MGSTEGLKRG LTVTSTNAPI SVPVGTATL GRIMDVLGRP IDEAGPVATE ERLPIHRQAP SYAEQAASTD LLETGIKVID LLCPFAKGGK VGLFGGAGVG K TVNMMELI ...String:
MHHHHHHSSG RIIQIIGAVI DVEFERTSVP KIYDALQVDG TETTLEVQQQ LGDGVVRTIA MGSTEGLKRG LTVTSTNAPI SVPVGTATL GRIMDVLGRP IDEAGPVATE ERLPIHRQAP SYAEQAASTD LLETGIKVID LLCPFAKGGK VGLFGGAGVG K TVNMMELI NNIAKAHSGL SVFAGVGERT REGNDFYHEM KDSNVLDKVA MVYGQMNEPP GNRLRVALTG LTMAEYFRDE KD ENGKGRD VLLFVDNIYR YTLAGTEVSA LLGRMPSAVG YQPTLAEEMG VLQERITSTK SGSITSIQAV YVPADDLTDP SPA TTFAHL DATVVLSRDI ASSGIYPAID PLDSTSRQLD PLVVGQEHYE IARAVQNVLQ RYKELKDIIA ILGMDELAEE DKLV VYRAR KIQRFFSQPF HVAEVFTGAP GKLVPLKETI RGFKGLLAGE YDHIPEQAFY MVGGIDEVIA KAEKL

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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB5075 (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
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 #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)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
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

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris hydrochloride
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
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: 5455 / Average electron dose: 64.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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: 1729782
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 139535
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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