+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34066 | |||||||||
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Title | F1-ATPase of Acinetobacter baumannii | |||||||||
Map data | Composite map of consensus maps 1 and 2 | |||||||||
Sample |
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Keywords | F1-ATPase / Acinetobacter baumannii / Hydrolase | |||||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / 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 | |||||||||
Biological species | Acinetobacter baumannii (bacteria) / Acinetobacter baumannii AB5075 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Saw W-G / Grueber G | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34066.map.gz | 150.7 MB | EMDB map data format | |
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Header (meta data) | emd-34066-v30.xml emd-34066.xml | 31.6 KB 31.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34066_fsc.xml emd_34066_fsc_2.xml | 12.3 KB 12.4 KB | Display Display | FSC data file |
Images | emd_34066.png | 156.5 KB | ||
Masks | emd_34066_msk_1.map emd_34066_msk_2.map | 160.8 MB 160.8 MB | Mask map | |
Filedesc metadata | emd-34066.cif.gz | 7.3 KB | ||
Others | emd_34066_additional_1.map.gz emd_34066_additional_2.map.gz emd_34066_additional_3.map.gz emd_34066_additional_4.map.gz emd_34066_half_map_1.map.gz emd_34066_half_map_2.map.gz | 146.7 MB 148.7 MB 138.7 MB 138.7 MB 146.2 MB 146.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34066 | HTTPS FTP |
-Validation report
Summary document | emd_34066_validation.pdf.gz | 970.7 KB | Display | EMDB validaton report |
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Full document | emd_34066_full_validation.pdf.gz | 970.2 KB | Display | |
Data in XML | emd_34066_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | emd_34066_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34066 | HTTPS FTP |
-Related structure data
Related structure data | 7yryMC 8hgxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34066.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map of consensus maps 1 and 2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8584 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34066_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_34066_msk_2.map | ||||||||||||
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Density Histograms |
-Additional map: Consensus map 1
File | emd_34066_additional_1.map | ||||||||||||
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Annotation | Consensus map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus map 2
File | emd_34066_additional_2.map | ||||||||||||
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Annotation | Consensus map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus map 2 half map 1
File | emd_34066_additional_3.map | ||||||||||||
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Annotation | Consensus map 2 half map 1 | ||||||||||||
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Density Histograms |
-Additional map: Consensus map 2 half map 2
File | emd_34066_additional_4.map | ||||||||||||
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Annotation | Consensus map 2 half map 2 | ||||||||||||
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Density Histograms |
-Half map: Consensus map 1 half map 2
File | emd_34066_half_map_1.map | ||||||||||||
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Annotation | Consensus map 1 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Consensus map 1 half map 1
File | emd_34066_half_map_2.map | ||||||||||||
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Annotation | Consensus map 1 half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : F1-ATPase of Acinetobacter baumannii
Entire | Name: F1-ATPase of Acinetobacter baumannii |
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Components |
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-Supramolecule #1: F1-ATPase of Acinetobacter baumannii
Supramolecule | Name: F1-ATPase of Acinetobacter baumannii / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Acinetobacter baumannii (bacteria) / Strain: AB5075 |
Molecular weight | Theoretical: 363.5 KDa |
-Macromolecule #1: ATP synthase subunit alpha
Macromolecule | Name: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: Acinetobacter baumannii AB5075 (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 |
Molecular weight | Theoretical: 55.452906 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: ATP synthase subunit beta
Macromolecule | Name: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii AB5075 (bacteria) |
Molecular weight | Theoretical: 51.156055 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: ATP synthase epsilon chain
Macromolecule | Name: ATP synthase epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii AB5075 (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 |
Molecular weight | Theoretical: 14.551682 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MATMQCDVVS VKESIYSGAV TMLIAKGAGG ELGILPGHAP LVTLLQPGPI RVLLENGTEE IVYVSGGVLE VQPHVVTVLA DTAIRADNL DEAAILEARK NAEQLLANQK SDLDSAAALA ALAETAAQLE TIRKIKNRAQ UniProtKB: ATP synthase epsilon chain |
-Macromolecule #4: ATP synthase gamma chain
Macromolecule | Name: ATP synthase gamma chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Acinetobacter baumannii AB5075 (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 |
Molecular weight | Theoretical: 32.135037 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #8: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |