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- EMDB-66242: Subtomogram averaged A, P state of the 80S ribosome in rat hippoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-66242
TitleSubtomogram averaged A, P state of the 80S ribosome in rat hippocampal neuron
Map data
Sample
  • Cell: neuronal cells treated with and without Puromycin
Keywordsribosome / neuronal cells / Puromycin
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsXing W / Chen C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2026
Title: rRNA expansion segments mediate ribosome dimerization as a conserved stress response.
Authors: Wenhong Jiang / Chen Chen / Xing Wang / Wei Huang / Dawid Krokowski / Ziyao Chen / Jiahao Xie / Zhaoming Su / Maria Hatzoglou / Derek J Taylor / Qiang Guo /
Abstract: Inhibition of messenger RNA translation is a common feature in proteostatic stress cellular responses. Puromycin, a widely used compound for studying translation, disrupts protein synthesis by ...Inhibition of messenger RNA translation is a common feature in proteostatic stress cellular responses. Puromycin, a widely used compound for studying translation, disrupts protein synthesis by mimicking the 3' end of aminoacyl-transfer RNAs. Despite its extensive use as a research tool to probe the connection between translation activity and various physiological and pathological states, the cellular response associated with puromycin-induced translation stress remains incompletely understood. Here, we used electron tomography and topology analysis to define the effects of puromycin on the translation machinery in situ. We show that puromycin-treated neuronal cells exhibit an accumulation of eIF5A-bound ribosomes in a translationally inactive "idle" state, and thereby defining a broader role of eIF5A in ribosome homeostasis. Additionally, the idle ribosomes formed dimeric complexes mediated by ribosomal RNA expansion segments, suggesting an evolved mechanism involving these regions in translational hibernating and protecting idle ribosomes. We further show that the hibernating disome formation is not unique to puromycin administration but represents a conserved mechanism as a response to different cellular stressors including endoplasmic reticulum stress and amino acid depletion. Collectively, our findings illuminate distinct states of mammalian ribosome hibernation and dimerization, providing new insights into the relationship of cellular stress and the dynamic regulation of ribosomal activity.
History
DepositionSep 18, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66242.png

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Map

FileDownload / File: emd_66242.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 196 pix.
= 537.04 Å		2.74 Å/pix.
x 196 pix.
= 537.04 Å		2.74 Å/pix.
x 196 pix.
= 537.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.93914646 - 2.3636572
Average (Standard dev.)0.02223013 (±0.20486677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 537.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66242_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_66242_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : neuronal cells treated with and without Puromycin

EntireName: neuronal cells treated with and without Puromycin
Components
  • Cell: neuronal cells treated with and without Puromycin

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Supramolecule #1: neuronal cells treated with and without Puromycin

SupramoleculeName: neuronal cells treated with and without Puromycin / type: cell / 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
Processingsubtomogram averaging
Aggregation statecell

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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 (6k x 4k) / Average electron dose: 2.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 2127
ExtractionNumber tomograms: 113 / Number images used: 31863 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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