+Open data
-Basic information
Entry | Database: PDB / ID: 7y5a | ||||||
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Title | Cryo-EM structure of the Mycolicibacterium smegmatis F1-ATPase | ||||||
Components |
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Keywords | HYDROLASE / Complex / F-ATP synthase / cryo-EM / mycobacteria | ||||||
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 | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Wong, C.F. / Saw, W.-G. / Grueber, G. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Antimicrob Agents Chemother / Year: 2022 Title: Structural Elements Involved in ATP Hydrolysis Inhibition and ATP Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-ATP Synthase Decipher New Targets for Inhibitors. Authors: Chui Fann Wong / Wuan-Geok Saw / Sandip Basak / Mio Sano / Hiroshi Ueno / Hwee Wen Kerk / Dennis Litty / Priya Ragunathan / Thomas Dick / Volker Müller / Hiroyuki Noji / Gerhard Grüber / Abstract: The FF-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the ...The FF-ATP synthase is required for the viability of tuberculosis (TB) and nontuberculous mycobacteria (NTM) and has been validated as a drug target. Here, we present the cryo-EM structures of the Mycobacterium smegmatis F-ATPase and the FF-ATP synthase with different nucleotide occupation within the catalytic sites and visualize critical elements for latent ATP hydrolysis and efficient ATP synthesis. Mutational studies reveal that the extended C-terminal domain (αCTD) of subunit α is the main element for the self-inhibition mechanism of ATP hydrolysis for TB and NTM bacteria. Rotational studies indicate that the transition between the inhibition state by the αCTD and the active state is a rapid process. We demonstrate that the unique mycobacterial γ-loop and subunit δ are critical elements required for ATP formation. The data underline that these mycobacterium-specific elements of α, γ, and δ are attractive targets, providing a platform for the discovery of species-specific inhibitors. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y5a.cif.gz | 526.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y5a.ent.gz | 432.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y5a_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7y5a_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7y5a_validation.xml.gz | 92.9 KB | Display | |
Data in CIF | 7y5a_validation.cif.gz | 138.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/7y5a ftp://data.pdbj.org/pub/pdb/validation_reports/y5/7y5a | HTTPS FTP |
-Related structure data
Related structure data | 33614MC 7y5bC 7y5cC 7y5dC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase subunit ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 58951.461 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: atpA, MSMEG_4938, MSMEI_4811 / Plasmid: pYUB1049 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc(2)4517 References: UniProt: A0R202, H+-transporting two-sector ATPase #2: Protein | Mass: 52499.332 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: atpD, MSMEG_4936, MSMEI_4809 / Plasmid: pYUB1049 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc(2)4517 References: UniProt: A0R200, H+-transporting two-sector ATPase |
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-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 33439.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: atpG, MSMEG_4937, MSMEI_4810 / Plasmid: pYUB1049 / Production host: Mycolicibacterium smegmatis (bacteria) / Strain (production host): mc(2)4517 / References: UniProt: A0R201 |
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-Non-polymers , 3 types, 10 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | |
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-Details
Has ligand of interest | Y |
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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: F1-ATPase / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.38 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: mc(2)155 | |||||||||||||||
Source (recombinant) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: mc(2)4517 / Plasmid: pYUB1049 | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2318 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 972956 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119732 / Num. of class averages: 1 / Symmetry type: POINT |