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- EMDB-54753: 80S ribosome of young S. cerevisiae cells (day 0) - polysome fraction -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54753
Title80S ribosome of young S. cerevisiae cells (day 0) - polysome fraction
Map data
Sample
  • Complex: 80S ribosome from Saccharomyces cerevisiae
Keywordsyeast / ubiquitination / translation / aging / RIBOSOME
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsKhusainov I / Beck M
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)724349-Complex assemblyEuropean Union
Max Planck Society Germany
CitationJournal: To Be Published
Title: Integrative analysis of the co-translational ubiquitinome reveals age-associated defects in protein biogenesis.
Authors: Seidel M / Li S / Geissler K / Khusainov I / Kucherenko Z / Becker A / Welther DK / Provaznik J / Heck J / Wu J / Langer JD / Benes V / Savitski MM / Frydman J / Beck M / Steinmetz LM
History
DepositionAug 10, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54753.png

Downloads & links

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Map

FileDownload / File: emd_54753.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å		0.83 Å/pix.
x 512 pix.
= 425.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.231
Minimum - Maximum-0.33446258 - 0.6870707
Average (Standard dev.)0.0012968275 (±0.030691145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54753_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54753_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ribosome from Saccharomyces cerevisiae

EntireName: 80S ribosome from Saccharomyces cerevisiae
Components
  • Complex: 80S ribosome from Saccharomyces cerevisiae

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Supramolecule #1: 80S ribosome from Saccharomyces cerevisiae

SupramoleculeName: 80S ribosome from Saccharomyces cerevisiae / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHepes-KOHhepes
140.0 mMKClpotassium chloride
10.0 mMMgCl2magnesium chloride
0.01 %NP40IGEPAL

Details: 20 mM Hepes-KOH pH 7.5, 140 mM KCL, 10 mM MgCl2, 0.01% IGEPAL
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9280 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 561844
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 287295
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4u3u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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