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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: To Be Published
Title: Polysome collapse and RNA condensation fluidize the cytoplasm
Authors: Xie Y / Shu T / Liu T / Spindler MC / Mahamid J / Hocky G / Holt LJ
History
DepositionMay 24, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50415.png

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.)
3.43 Å/pix.
x 176 pix.
= 602.8 Å		3.43 Å/pix.
x 176 pix.
= 602.8 Å		3.43 Å/pix.
x 176 pix.
= 602.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.425 Å
Density

Histogram

Histogram (log scale)
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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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

Fileemd_50415_half_map_2.map
AnnotationSecond half map of subtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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