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- EMDB-76379: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnes... -

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Basic information

Entry
Database: EMDB / ID: EMD-76379
TitleRat 80S ribosome purified from brain RNA granules at 10 mM Magnesium. Class 2 80S with PP tRNA
Map data
Sample
  • Complex: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnesium. Class 2 80S with PP tRNA
KeywordsRibosome / neuron / translation
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOrtega J / Sun J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Elife / Year: 2026
Title: FMRP regulates neuronal RNA granules containing stalled ribosomes, not where ribosomes stall.
Authors: Jewel T-Y Li / Mehdi Amiri / Senthilkumar Kailasam / Lily Drever / Jingyu Sun / Laura Bohorquez / Nahum Sonenberg / Joaquin Ortega / Wayne S Sossin /
Abstract: Local protein synthesis is a crucial process that maintains local proteostasis in neurons. A large percentage of mRNAs translated in developing neurons are associated with stalled ribosomes. FMRP, ...Local protein synthesis is a crucial process that maintains local proteostasis in neurons. A large percentage of mRNAs translated in developing neurons are associated with stalled ribosomes. FMRP, the protein lost in Fragile X syndrome, is highly enriched in RNA granules that contain stalled ribosomes. Previous examination of ribosome-protected fragments (RPFs) from stalled neuronal ribosomes identified sequences that match those found in mRNAs associated with FMRP. To investigate whether FMRP recognition of these sequences is important for determining where ribosomes stall on mRNAs, we examined RPFs isolated from P5 mice of both sexes that lack the FMRP protein. The loss of FMRP had no significant effect on the proteins associated with neuronal stalled ribosomes, on ribosome structure, or the stalling sites (locations where RPFs accumulated). There was a small, but significant decrease in the number of RPFs from mRNAs previously shown to be associated with FMRP by CLIP. Additionally, the number of neuronal RNA granules containing stalled ribosomes, as assayed by ribopuromycylation, decreased. These results suggest a role of FMRP in neuronal RNA granules that contain stalled ribosomes, though loss of FMRP does not influence where ribosomes are stalled or the formation of stalled ribosome.
History
DepositionMar 30, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76379.png

Downloads & links

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Map

FileDownload / File: emd_76379.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 448 pix.
= 488.32 Å		1.09 Å/pix.
x 448 pix.
= 488.32 Å		1.09 Å/pix.
x 448 pix.
= 488.32 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.2327766 - 0.98963845
Average (Standard dev.)0.0071191513 (±0.053277355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 488.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_76379_additional_1.map
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Additional map: #2

Fileemd_76379_additional_2.map
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Additional map: #3

Fileemd_76379_additional_3.map
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Half map: #1

Fileemd_76379_half_map_1.map
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Half map: #2

Fileemd_76379_half_map_2.map
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Sample components

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Entire : Rat 80S ribosome purified from brain RNA granules at 10 mM Magnes...

EntireName: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnesium. Class 2 80S with PP tRNA
Components
  • Complex: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnesium. Class 2 80S with PP tRNA

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Supramolecule #1: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnes...

SupramoleculeName: Rat 80S ribosome purified from brain RNA granules at 10 mM Magnesium. Class 2 80S with PP tRNA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 141803
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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