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Yorodumi- EMDB-23765: The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23765 | |||||||||||||||||||||||||||
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Title | The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase | |||||||||||||||||||||||||||
Map data | Globally sharpened map. | |||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information : / : / : / : / : / : / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism ...: / : / : / : / : / : / proton motive force-driven 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 / proton motive force-driven mitochondrial ATP synthesis / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||||||||
Authors | Guo H / Rubinstein JL | |||||||||||||||||||||||||||
Funding support | Canada, United States, 8 items
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Citation | Journal: Nat Chem Biol / Year: 2022 Title: Apoptolidin family glycomacrolides target leukemia through inhibition of ATP synthase. Authors: Benjamin J Reisman / Hui Guo / Haley E Ramsey / Madison T Wright / Bradley I Reinfeld / P Brent Ferrell / Gary A Sulikowski / W Kimryn Rathmell / Michael R Savona / Lars Plate / John L ...Authors: Benjamin J Reisman / Hui Guo / Haley E Ramsey / Madison T Wright / Bradley I Reinfeld / P Brent Ferrell / Gary A Sulikowski / W Kimryn Rathmell / Michael R Savona / Lars Plate / John L Rubinstein / Brian O Bachmann / Abstract: Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene- ...Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene-transformed cells, yet their molecular mechanism remains uncertain. We used photoaffinity analogs of the apoptolidins to identify the F subcomplex of mitochondrial ATP synthase as the target of apoptolidin A. Cryogenic electron microscopy (cryo-EM) of apoptolidin and ammocidin-ATP synthase complexes revealed a novel shared mode of inhibition that was confirmed by deep mutational scanning of the binding interface to reveal resistance mutations which were confirmed using CRISPR-Cas9. Ammocidin A was found to suppress leukemia progression in vivo at doses that were tolerated with minimal toxicity. The combination of cellular, structural, mutagenesis, and in vivo evidence defines the mechanism of action of apoptolidin family glycomacrolides and establishes a path to address oxidative phosphorylation-dependent cancers. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23765.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-23765-v30.xml emd-23765.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23765_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_23765.png | 77.2 KB | ||
Masks | emd_23765_msk_1.map | 64 MB | Mask map | |
Others | emd_23765_additional_1.map.gz emd_23765_half_map_1.map.gz emd_23765_half_map_2.map.gz | 32.3 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23765 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23765 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23765.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Globally sharpened map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23765_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map.
File | emd_23765_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1.
File | emd_23765_half_map_1.map | ||||||||||||
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Annotation | Half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2.
File | emd_23765_half_map_2.map | ||||||||||||
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Annotation | Half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase
Entire | Name: The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase |
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Components |
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-Supramolecule #1: The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase
Supramolecule | Name: The F1 region of inhibitor-free Saccharomyces cerevisiae ATP synthase type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006 |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 190 / Average exposure time: 15.0 sec. / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Calibrated defocus max: 3.2 µm / Calibrated magnification: 34483 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus min: 1.0 µm / Nominal magnification: 25000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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