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- EMDB-55098: Naked mole-rat 80S ribosome in pre-translocation rotated hybrid state -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-55098
TitleNaked mole-rat 80S ribosome in pre-translocation rotated hybrid state
Map data
Sample
  • Complex: 80S ribosome
Keywordsnaked mole-rat / ribosome / 80S
Biological speciesHeterocephalus glaber (naked mole-rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsGul M / Kudryashev M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU3222/3-1 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structure of the naked mole-rat ribosome reveals a stabilized split 28S rRNA.
Authors: Mehmet Gül / Alice Rossi / Christian M T Spahn / Gary R Lewin / Mikhail Kudryashev /
Abstract: The naked mole-rat (Heterocephalus glaber) is a long-lived mammal with resistance to cancer and hypoxia, suggesting the evolution of robust proteostasis networks. The ribosome, central for protein ...The naked mole-rat (Heterocephalus glaber) is a long-lived mammal with resistance to cancer and hypoxia, suggesting the evolution of robust proteostasis networks. The ribosome, central for protein synthesis, is key to cellular stress responses and has an unusual feature: the 28S rRNA split; however, the details of its organization remain unknown. Here, we present high-resolution cryo-EM structures of the naked mole-rat 80S ribosome in four states of the elongation cycle. The structures reveal a conserved overall architecture and rRNA modification landscape compared to other mammals, and provide an atomic-level view of the distinct break in the 28S rRNA. This cleavage event, located in the D6 expansion segment, is structurally stabilized by a network of interactions with surrounding ribosomal proteins, maintaining the integrity of the large subunit. Our comparative analysis revealed that this compensatory network preserves a canonical architecture that is nearly indistinguishable from intact mouse and human ribosomes. These findings resolve the structural basis of this distinct cleavage, showing that it is a stable, integrated feature whose function is likely linked to more subtle regulatory mechanisms, rather than inducing major structural rearrangements.
History
DepositionSep 18, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55098.png

Downloads & links

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Map

FileDownload / File: emd_55098.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.62
Minimum - Maximum-2.327787 - 6.2653975
Average (Standard dev.)0.016310167 (±0.17665134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55098_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55098_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : 80S ribosome

EntireName: 80S ribosome
Components
  • Complex: 80S ribosome

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Heterocephalus glaber (naked mole-rat) / Organ: liver

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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 (6k x 4k) / Average electron dose: 60.04 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 340823
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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