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- EMDB-50415: Subtomogram average of 80S ribosomes in S. cerevisiae under acute... -

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Basic information

Entry
Database: EMDB / ID: EMD-50415
TitleSubtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Map dataSubtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Sample
  • Cell: Cryo-focused ion beam milled lamellae of S.cerevisiae cells under acute glucose starvation
KeywordsGlobular protein / translation / RIBOSOME
Biological speciesS.cerevisiae (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsSpindler MC / Mahamid J
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: Mol Cell / Year: 2024
Title: Polysome collapse and RNA condensation fluidize the cytoplasm.
Authors: Ying Xie / Tong Shu / Tiewei Liu / Marie-Christin Spindler / Julia Mahamid / Glen M Hocky / David Gresham / Liam J Holt /
Abstract: The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to ...The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
History
DepositionMay 24, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_50415.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.05 Å/pix.
x 60 pix.
= 423. Å
7.05 Å/pix.
x 60 pix.
= 423. Å
7.05 Å/pix.
x 60 pix.
= 423. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.3.4253.4253.425
CCP4 map header7.057.057.05
Density
Contour LevelBy AUTHOR: 0.0054
Minimum - Maximum-0.005784557 - 0.023328058
Average (Standard dev.)-0.00006523494 (±0.0019735298)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 602.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50415_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: First half map of subtomogram average of 80S...

Fileemd_50415_half_map_1.map
AnnotationFirst half map of subtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Cryo-focused ion beam milled lamellae of S.cerevisiae cells under...

EntireName: Cryo-focused ion beam milled lamellae of S.cerevisiae cells under acute glucose starvation
Components
  • Cell: Cryo-focused ion beam milled lamellae of S.cerevisiae cells under acute glucose starvation

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Supramolecule #1: Cryo-focused ion beam milled lamellae of S.cerevisiae cells under...

SupramoleculeName: Cryo-focused ion beam milled lamellae of S.cerevisiae cells under acute glucose starvation
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: S.cerevisiae (yeast) / Strain: BY4741

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.11792 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 51821
ExtractionNumber tomograms: 10 / Number images used: 53596 / Method: DeePiCt 3D CNN + manual / Software - Name: Warp (ver. 1.0.9)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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