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Yorodumi- EMDB-33615: Cryo-EM structure of F-ATP synthase from Mycolicibacterium smegma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33615 | |||||||||
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Title | Cryo-EM structure of F-ATP synthase from Mycolicibacterium smegmatis (rotational state 1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / F-ATP synthase / cryo-EM / mycobacteria / HYDROLASE | |||||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / 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 / hydrolase activity ...proton motive force-driven plasma membrane ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem II / 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 / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Saw W-G / Wong CF / Grueber G | |||||||||
Funding support | Singapore, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33615.map.gz | 22.2 MB | EMDB map data format | |
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Header (meta data) | emd-33615-v30.xml emd-33615.xml | 31.3 KB 31.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33615_fsc.xml | 15.7 KB | Display | FSC data file |
Images | emd_33615.png | 128.2 KB | ||
Masks | emd_33615_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-33615.cif.gz | 8.2 KB | ||
Others | emd_33615_half_map_1.map.gz emd_33615_half_map_2.map.gz | 260.1 MB 260.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33615 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33615 | HTTPS FTP |
-Validation report
Summary document | emd_33615_validation.pdf.gz | 885.3 KB | Display | EMDB validaton report |
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Full document | emd_33615_full_validation.pdf.gz | 884.8 KB | Display | |
Data in XML | emd_33615_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | emd_33615_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33615 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33615 | HTTPS FTP |
-Related structure data
Related structure data | 7y5bMC 7y5aC 7y5cC 7y5dC 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_33615.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33615_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33615_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33615_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : F-ATP synthase
+Supramolecule #1: F-ATP synthase
+Macromolecule #1: ATP synthase subunit alpha
+Macromolecule #2: ATP synthase subunit alpha
+Macromolecule #3: ATP synthase subunit beta
+Macromolecule #4: ATP synthase gamma chain
+Macromolecule #5: ATP synthase epsilon chain
+Macromolecule #6: ATP synthase subunit a
+Macromolecule #7: ATP synthase subunit b
+Macromolecule #8: ATP synthase subunit b-delta
+Macromolecule #9: ATP synthase subunit c
+Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / 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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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3663 / Average electron dose: 38.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |