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- EMDB-4377: Tomogram obtained for yeast cells treated with rapamycin -

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Basic information

Entry
Database: EMDB / ID: 4377
TitleTomogram obtained for yeast cells treated with rapamycin
Map dataTomogram obtained for yeast cells treated with rapamycin
SampleYeast cell treated with rapamycin:
SourceSaccharomyces cerevisiae W303 (yeast)
Methodelectron tomography / cryo EM
AuthorsPfeffer S / Engel BD / Schaffer M
CitationJournal: 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.
DateDeposition: Apr 16, 2018 / Header (metadata) release: May 23, 2018 / Map release: Jun 27, 2018 / Last update: Jul 25, 2018

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

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Map

Fileemd_4377.map.gz (map file in CCP4 format, 1267004 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
371 pix
13.68 Å/pix.
= 5075.28 Å
924 pix
13.68 Å/pix.
= 12640.32 Å
924 pix
13.68 Å/pix.
= 12640.32 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 13.68 Å
Density
Minimum - Maximum-0.5459763 - 0.6919633
Average (Standard dev.)0.00029750084 (0.07987138)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions924924371
Origin0.0.0.
Limit923.923.370.
Spacing924924371
CellA: 12640.32 Å / B: 12640.32 Å / C: 5075.2803 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.6813.6813.68
M x/y/z924924371
origin x/y/z0.0000.0000.000
length x/y/z12640.32012640.3205075.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS924924371
D min/max/mean-0.5460.6920.000

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Supplemental data

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Sample components

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Entire Yeast cell treated with rapamycin

EntireName: Yeast cell treated with rapamycin / Number of components: 1

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Component #1: cellular-component, Yeast cell treated with rapamycin

Cellular-componentName: Yeast cell treated with rapamycin / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Details: 10 seconds blot time, blot force 10.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 6000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 61
3D reconstructionAlgorithm: BACK PROJECTION

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