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- EMDB-40345: terminating rabbit ribosome with SRI-41315 (focused on ABCE1) -

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Basic information

Entry
Database: EMDB / ID: EMD-40345
Titleterminating rabbit ribosome with SRI-41315 (focused on ABCE1)
Map dataunsharpened map
Sample
  • Complex: terminating rabbit ribosome
Keywordstermination / SRI-41315 / RIBOSOME
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYip MCJ / Coelho JPL / Oltion K / Tauton J / Shao S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415 United States
David and Lucile Packard Foundation United States
American Heart Association287375208 United States
CitationJournal: Nat Chem Biol / Year: 2024
Title: The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center.
Authors: João P L Coelho / Matthew C J Yip / Keely Oltion / Jack Taunton / Sichen Shao /
Abstract: Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires ...Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1.
History
DepositionApr 5, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40345.png

Downloads & links

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Map

FileDownload / File: emd_40345.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.015306157 - 0.055031143
Average (Standard dev.)0.00026487565 (±0.0030550908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_40345_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Additional map: deepEM processed map

Fileemd_40345_additional_2.map
AnnotationdeepEM processed map
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Half map: half1 map

Fileemd_40345_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half2 map

Fileemd_40345_half_map_2.map
Annotationhalf2 map
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Sample components

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Entire : terminating rabbit ribosome

EntireName: terminating rabbit ribosome
Components
  • Complex: terminating rabbit ribosome

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Supramolecule #1: terminating rabbit ribosome

SupramoleculeName: terminating rabbit ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#87
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 4 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10181

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51942
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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