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- EMDB-19924: New1 bound to 80S ribosome; eRF1, P-tRNA, E-tRNA (State 7) -

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Basic information

Entry
Database: EMDB / ID: EMD-19924
TitleNew1 bound to 80S ribosome; eRF1, P-tRNA, E-tRNA (State 7)
Map data
Sample
  • Complex: Ex vivo pullout of New1
KeywordsRIBOSOME / New1 / Translation termination / 80S
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsPaternoga H / Pochopien AA / Wilson DN
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3285/11-1 Germany
CitationJournal: bioRxiv / Year: 2024
Title: The ABCF ATPase New1 resolves translation termination defects associated with specific tRNA and tRNA isoacceptors in the P site.
Authors: Kathryn Turnbull / Helge Paternoga / Esther von der Weth / Artyom A Egorov / Agnieszka A Pochopien / Yujie Zhang / Lilit Nersisyan / Tõnu Margus / Marcus J O Johansson / Vicent Pelechano / ...Authors: Kathryn Turnbull / Helge Paternoga / Esther von der Weth / Artyom A Egorov / Agnieszka A Pochopien / Yujie Zhang / Lilit Nersisyan / Tõnu Margus / Marcus J O Johansson / Vicent Pelechano / Daniel N Wilson / Vasili Hauryliuk /
Abstract: The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are ...The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.
History
DepositionMar 23, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19924.png

Downloads & links

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Map

FileDownload / File: emd_19924.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 455.28 Å		1.08 Å/pix.
x 420 pix.
= 455.28 Å		1.08 Å/pix.
x 420 pix.
= 455.28 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.019324781 - 0.043485142
Average (Standard dev.)0.00017688936 (±0.0036881643)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 455.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local resolution filtered map

Fileemd_19924_additional_1.map
AnnotationLocal resolution filtered map
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Half map: #1

Fileemd_19924_half_map_1.map
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Half map: #2

Fileemd_19924_half_map_2.map
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Sample components

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Entire : Ex vivo pullout of New1

EntireName: Ex vivo pullout of New1
Components
  • Complex: Ex vivo pullout of New1

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Supramolecule #1: Ex vivo pullout of New1

SupramoleculeName: Ex vivo pullout of New1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

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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

BufferpH: 7.4
GridModel: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v88

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5613
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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