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- EMDB-4372: Ribosome subtomogram average obtained for control yeast cells -

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Basic information

Entry
Database: EMDB / ID: 4372
TitleRibosome subtomogram average obtained for control yeast cells
Map dataRibosome subtomogram average obtained for control yeast cells
SampleCytosolic 80S ribosome:
SourceSaccharomyces cerevisiae W303 (yeast)
Methodsubtomogram averaging / cryo EM / 11.5 Å resolution
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 16, 2018 / Map release: Jun 27, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4372.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.42 Å/pix.
= 437.76 Å
128 pix
3.42 Å/pix.
= 437.76 Å
128 pix
3.42 Å/pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-1.098915 - 1.5347656
Average (Standard dev.)0.0008373331 (0.14218503)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.0.0.
Limit127.127.127.
Spacing128128128
CellA=B=C: 437.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.0991.5350.001

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Supplemental data

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Sample components

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Entire Cytosolic 80S ribosome

EntireName: Cytosolic 80S ribosome / Number of components: 1

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Component #1: protein, Cytosolic 80S ribosome

ProteinName: Cytosolic 80S ribosome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / 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: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 36974
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF

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