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

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Open data


ID or keywords:

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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: To Be Published
Title: Naked mole-rat 80S ribosome in pre-translocation rotated hybrid state
Authors: Gul M / Kudryashev M
History
DepositionSep 18, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 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)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55098_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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