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- EMDB-19950: Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR) -

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Basic information

Entry
Database: EMDB / ID: EMD-19950
TitleYeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)
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 posttranslocation non-rotated P/P (POST2-NR)
Keywordsribosome / urm / ncs2ncs6 / elp / elongator / tRNA modification / tRNA thiolation / tRNA recognition / TRANSLATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsKoziej L / Glatt S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101001394European Union
Citation
Journal: Nucleic Acids Res / Year: 2025
Title: Suboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants.
Authors: Jie Wu / Cristian Eggers / Olga Sin / Łukasz Koziej / Hector Mancilla / Fabienne Mollet / Hans R Schöler / Hannes C A Drexler / Tristan Ranff / Christian Fufezan / Claudine Kraft / ...Authors: Jie Wu / Cristian Eggers / Olga Sin / Łukasz Koziej / Hector Mancilla / Fabienne Mollet / Hans R Schöler / Hannes C A Drexler / Tristan Ranff / Christian Fufezan / Claudine Kraft / Sebastian Glatt / Jan M Bruder / Sebastian A Leidel /
Abstract: Transfer RNA (tRNA) modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding. However, the mechanisms by which tRNA modifications modulate codon ...Transfer RNA (tRNA) modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding. However, the mechanisms by which tRNA modifications modulate codon optimality and trigger phenotypes remain unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs in wobble uridine modification (U34) mutants. This triggers ribosome collisions and a coordinated hierarchical response of cellular quality control pathways. High-resolution ribosome profiling reveals an unexpected functional diversity of U34 modifications during decoding. For instance, 5-carbamoylmethyluridine (ncm5U) exhibits distinct effects at the A and P sites. Importantly, ribosomes only slow down at a fraction of codons decoded by hypomodified tRNA, and the decoding speed of most codons remains unaffected. However, the translation speed of a codon largely depends on the identity of A- and P-site codons. Stalling at modification-dependent codon pairs induces ribosome collisions, triggering ribosome-associated quality control (RQC) and preventing protein aggregation by degrading aberrant nascent peptides and messenger RNAs. Inactivation of RQC stimulates the expression of molecular chaperones that remove protein aggregates. Our results demonstrate that loss of tRNA modifications primarily disrupts translation rates of suboptimal codon pairs, showing the coordinated regulation and adaptability of cellular surveillance systems. These systems ensure efficient and accurate protein synthesis and maintain protein homeostasis.
#1: Journal: 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-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19950.png

Downloads & links

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Map

FileDownload / File: emd_19950.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
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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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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8456 Å
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Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.009358235 - 2.6952717
Average (Standard dev.)0.006838464 (±0.06741807)
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_19950_msk_1.map
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Mask #2

Fileemd_19950_msk_2.map
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Additional map: Combined half maps post-processed using sharpening B factor 34.5.

Fileemd_19950_additional_1.map
AnnotationCombined half maps post-processed using sharpening B factor 34.5.
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Additional map: Map combined from 2 independent halves. Not post-processed.

Fileemd_19950_additional_2.map
AnnotationMap combined from 2 independent halves. Not post-processed.
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Half map: #2

Fileemd_19950_half_map_1.map
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Half map: #1

Fileemd_19950_half_map_2.map
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Sample components

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Entire : Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)

EntireName: Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)
Components
  • Complex: Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)

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Supramolecule #1: Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)

SupramoleculeName: Yeast 80S ribosome posttranslocation non-rotated P/P (POST2-NR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54
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: 36663 / 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: 6454715 / 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: 6 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Homogenous Refinement / Number images used: 79679
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: 12000 / 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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