|Entry||Database: EMDB / ID: 4373|
|Title||Ribosome subtomogram average obtained for yeast cells treated with rapamycin|
|Map data||Ribosome subtomogram average obtained for yeast cells treated with rapamycin|
|Sample||Cytosolic 80S ribosome:|
|Source||Saccharomyces cerevisiae W303 (yeast)|
|Method||subtomogram averaging / cryo EM / 11.5 Å resolution|
|Authors||Pfeffer S / Engel BD / Schaffer M|
|Citation||Journal: Cell / Year: 2018|
Title: mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding.
Authors: M Delarue / G P Brittingham / S Pfeffer / I V Surovtsev / S Pinglay / K J Kennedy / M Schaffer / J I Gutierrez / D Sang / G Poterewicz / J K Chung / J M Plitzko / J T Groves / C Jacobs-Wagner / B D Engel / L J Holt
Abstract: Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed ...Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
|Date||Deposition: Apr 16, 2018 / Header (metadata) release: May 23, 2018 / Map release: Jun 27, 2018 / Last update: Jul 25, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4373.map.gz (map file in CCP4 format, 8389 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.42 Å|
CCP4 map header:
-Entire Cytosolic 80S ribosome
|Entire||Name: Cytosolic 80S ribosome / Number of components: 1|
-Component #1: protein, Cytosolic 80S ribosome
|Protein||Name: Cytosolic 80S ribosome / Recombinant expression: No|
|Source||Species: Saccharomyces cerevisiae W303 (yeast)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Details: 10 seconds blot time, blot force 10.|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD / Defocus: 6000.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 18852|
|3D reconstruction||Algorithm: BACK PROJECTION / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF|
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