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- EMDB-19948: Yeast 80S ribosome (wild type) PRE-translocation-hybrid P/E A/A* ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19948
TitleYeast 80S ribosome (wild type) PRE-translocation-hybrid P/E A/A* (PRE-H2) dataset 2/2
Map dataMap combined from 2 independent halves and post-processed by DeepEMhancer with binary mask normalization mode using refinement mask.
Sample
  • Complex: Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)
Keywordsribosome / urm / ncs2ncs6 / elp / elongator / tRNA modification / tRNA thiolation / tRNA recognition / TRANSLATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsKoziej L / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
CitationJournal: Biorxiv / Year: 2024
Title: Codon Pair-Specific Translation Defects Trigger Ribosome-Associated Quality Control to Avoid Proteotoxic Stress
Authors: Koziej L / Glatt S
History
DepositionMar 26, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19948.png

Downloads & links

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Map

FileDownload / File: emd_19948.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap combined from 2 independent halves and post-processed by DeepEMhancer with binary mask normalization mode using refinement mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 600 pix.
= 507.36 Å		0.85 Å/pix.
x 600 pix.
= 507.36 Å		0.85 Å/pix.
x 600 pix.
= 507.36 Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8456 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.009265251 - 2.7277536
Average (Standard dev.)0.006781197 (±0.06726236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 507.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19948_msk_1.map
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AxesZYX

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Mask #2

Fileemd_19948_msk_2.map
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Additional map: Map combined from 2 independent halves. Not post-processed.

Fileemd_19948_additional_1.map
AnnotationMap combined from 2 independent halves. Not post-processed.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Combined half maps post-processed using sharpening B factor 38.8.

Fileemd_19948_additional_2.map
AnnotationCombined half maps post-processed using sharpening B factor 38.8.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_19948_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_19948_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)

EntireName: Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)
Components
  • Complex: Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)

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Supramolecule #1: Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)

SupramoleculeName: Yeast 80S ribosome PRE-translocation-hybrid P/E A/A* (PRE-H2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54 / Details: wild type strain
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741
Molecular weightTheoretical: 3.3 MDa

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
50.0 mMNH4Clammonium chloride
50.0 mMKClpotassium chloride
7.0 mMMgCl2magnesium chloride
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsConcentration of the sample: 20 A260 (absorbance at 260 nm, 10 mm path), 10 A280 (absorbance at 280 nm, 10 mm path)

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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) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 10009 / Average exposure time: 1.82 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
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: 1764637 / Details: Template Picking
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 8 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous Refinement / Number images used: 338070
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous Refinement
Final 3D classificationNumber classes: 10 / Avg.num./class: 45000 / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: 3D Class
Details: Focused/Masked 3D classification without angular assignment
FSC plot (resolution estimation)

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