+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33614 | |||||||||
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Title | Cryo-EM structure of the Mycolicibacterium smegmatis F1-ATPase | |||||||||
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 / 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 | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Wong CF / Saw W-G / 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_33614.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-33614-v30.xml emd-33614.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33614_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_33614.png | 118.6 KB | ||
Masks | emd_33614_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-33614.cif.gz | 7 KB | ||
Others | emd_33614_half_map_1.map.gz emd_33614_half_map_2.map.gz | 81 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33614 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33614 | HTTPS FTP |
-Validation report
Summary document | emd_33614_validation.pdf.gz | 909.4 KB | Display | EMDB validaton report |
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Full document | emd_33614_full_validation.pdf.gz | 909 KB | Display | |
Data in XML | emd_33614_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_33614_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33614 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33614 | HTTPS FTP |
-Related structure data
Related structure data | 7y5aMC 7y5bC 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_33614.map.gz / Format: CCP4 / Size: 103 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_33614_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33614_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33614_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : F1-ATPase
Entire | Name: F1-ATPase |
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Components |
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-Supramolecule #1: F1-ATPase
Supramolecule | Name: F1-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: mc(2)155 |
Molecular weight | Theoretical: 380 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: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 58.951461 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ ...String: MAELTISAAD IEGAIEDYVS SFSADTEREE IGTVIDAGDG IAHVEGLPSV MTQELLEFPG GVLGVALNLD EHSVGAVILG EFEKIEEGQ QVKRTGEVLS VPVGDAFLGR VVNPLGQPID GQGDIAAETR RALELQAPSV VQRQSVSEPL QTGIKAIDAM T PIGRGQRQ LIIGDRKTGK TAVCVDTILN QREAWLTGDP KQQVRCVYVA IGQKGTTIAS VKRALEEGGA MEYTTIVAAP AS DAAGFKW LAPYTGSAIG QHWMYNGKHV LIVFDDLSKQ ADAYRAISLL LRRPPGREAF PGDVFYLHSR LLERCAKLSD ELG GGSMTG LPIIETKAND ISAFIPTNVI SITDGQCFLE SDLFNQGVRP AINVGVSVSR VGGAAQIKAM KEVAGSLRLD LSQY RELEA FAAFASDLDA ASKAQLDRGA RLVELLKQPQ YSPLAVEEQV VAIFLGTQGH LDSVPVEDVQ RFESELLEHV KASHS DIFD GIRETKKLSE EAEEKLVSVI NEFKKGFQAS DGSSVVVSEN AEALDPEDLE KESVKVRKPA PKKA 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 / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 52.499332 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: MHHHHHHTAT AEKTAGRVVR ITGPVVDVEF PRGSVPELFN ALHAEITFGA LAKTLTLEVA QHLGDSLVRC ISMQPTDGLV RGVEVTDTG ASISVPVGDG VKGHVFNALG DCLDDPGYGK DFEHWSIHRK PPAFSDLEPR TEMLETGLKV VDLLTPYVRG G KIALFGGA ...String: MHHHHHHTAT AEKTAGRVVR ITGPVVDVEF PRGSVPELFN ALHAEITFGA LAKTLTLEVA QHLGDSLVRC ISMQPTDGLV RGVEVTDTG ASISVPVGDG VKGHVFNALG DCLDDPGYGK DFEHWSIHRK PPAFSDLEPR TEMLETGLKV VDLLTPYVRG G KIALFGGA GVGKTVLIQE MINRIARNFG GTSVFAGVGE RTREGNDLWV ELADANVLKD TALVFGQMDE PPGTRMRVAL SA LTMAEFF RDEQGQDVLL FIDNIFRFTQ AGSEVSTLLG RMPSAVGYQP TLADEMGELQ ERITSTRGRS ITSMQAVYVP ADD YTDPAP ATTFAHLDAT TELSRAVFSK GIFPAVDPLA SSSTILDPAI VGDEHYRVAQ EVIRILQRYK DLQDIIAILG IDEL SEEDK QLVNRARRIE RFLSQNMMAA EQFTGQPGST VPLKETIEAF DKLTKGEFDH LPEQAFFLIG GLDDLAKKAE SLGAK L UniProtKB: ATP synthase subunit beta |
-Macromolecule #3: ATP synthase gamma chain
Macromolecule | Name: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 33.439836 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis (bacteria) |
Sequence | String: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE ...String: MAATLRELRG RIRSAGSIKK ITKAQELIAT SRIAKAQARV EAARPYAAEI TNMLTELAGA SALDHPLLVE RKQPKRAGVL VVSSDRGLC GAYNANVLRR AEELFSLLRD EGKDPVLYVV GRKALGYFSF RQRTVVESWT GFSERPTYEN AREIADTLVN A FMAGADDE GDDAGADGIL GVDELHIVFT EFRSMLSQTA VARRAAPMEV EYVGEVETGP RTLYSFEPDP ETLFDALLPR YI ATRVYAA LLEAAASESA SRRRAMKSAT DNADDLIKAL TLAANRERQA QITQEISEIV GGANALAGSK UniProtKB: ATP synthase gamma chain |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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: 2318 / Average electron dose: 40.0 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 |