+Open data
-Basic information
Entry | Database: PDB / ID: 7p2y | ||||||
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Title | F1Fo-ATP synthase from Acinetobacter baumannii (state 1) | ||||||
Components | (ATP synthase ...) x 8 | ||||||
Keywords | MEMBRANE PROTEIN / ATP synthase / ESKAPE / Rotary ATP synthase / F1Fo / peptidisc / bioenergetics / IMP / multi-drug resistance / pathogenic | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / 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 / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Demmer, J.K. / Phillips, B.P. / Uhrig, O.L. / Filloux, A. / Allsopp, L.P. / Bublitz, M. / Meier, T. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structure of ATP synthase from ESKAPE pathogen . Authors: Julius K Demmer / Ben P Phillips / O Lisa Uhrig / Alain Filloux / Luke P Allsopp / Maike Bublitz / Thomas Meier / Abstract: The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate ...The global spread of multidrug-resistant infections urgently calls for the identification of novel drug targets. We solved the electron cryo-microscopy structure of the FF-adenosine 5'-triphosphate (ATP) synthase from in three distinct conformational states. The nucleotide-converting F subcomplex reveals a specific self-inhibition mechanism, which supports a unidirectional ratchet mechanism to avoid wasteful ATP consumption. In the membrane-embedded F complex, the structure shows unique structural adaptations along both the entry and exit pathways of the proton-conducting a-subunit. These features, absent in mitochondrial ATP synthases, represent attractive targets for the development of next-generation therapeutics that can act directly at the culmination of bioenergetics in this clinically relevant pathogen. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p2y.cif.gz | 801.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p2y.ent.gz | 665.9 KB | Display | PDB format |
PDBx/mmJSON format | 7p2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p2y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7p2y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7p2y_validation.xml.gz | 108.1 KB | Display | |
Data in CIF | 7p2y_validation.cif.gz | 173.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p2y ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p2y | HTTPS FTP |
-Related structure data
Related structure data | 13174MC 7p3nC 7p3wC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase ... , 8 types, 22 molecules ABCDEFGHJKLOPQRSabpdeg
#1: Protein | Mass: 55452.906 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M142, H+-transporting two-sector ATPase #2: Protein | Mass: 50327.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M144, H+-transporting two-sector ATPase #3: Protein | Mass: 8363.021 Da / Num. of mol.: 10 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M139 #4: Protein | | Mass: 32467.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M137 #5: Protein | Mass: 17009.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M140 #6: Protein | | Mass: 19525.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M141 #7: Protein | | Mass: 14551.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M145 #8: Protein | | Mass: 32135.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377 References: UniProt: A3M143 |
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-Non-polymers , 5 types, 12 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-ADP / | #12: Chemical | ChemComp-PO4 / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: F1Fo ATP synthase / Type: COMPLEX Details: State 1 of F1Fo ATP synthase from ESKAPE pathogen Acinetobacter baumannii Entity ID: #1-#8 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.528 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria) Strain: ATCC 17978 / Cellular location: Cell membrane | ||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was applied directly from gel filtration to ultra-thin carbon in peptidiscs. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: 4ul sample, blotted for 4s at a blotforce of -4. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Data collected at Diamond Light Source (Harwell, UK) using Titan Krios G3 and automated alignments using Sherpa. Detector used was Gatan K3 including energy filter. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 85000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11490 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 349160 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72317 / Num. of class averages: 1 / Symmetry type: POINT |