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- EMDB-55100: Naked mole-rat 80S ribosome in post-translocation non-rotated state -

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Basic information

Entry
Database: EMDB / ID: EMD-55100
TitleNaked mole-rat 80S ribosome in post-translocation non-rotated state
Map data
Sample
  • Complex: 80S ribosome
Keywordsnaked mole-rat / ribosome / 80S
Function / homology
Function and homology information


Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / SRP-dependent cotranslational protein targeting to membrane / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / 5.8S rRNA binding / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of protein neddylation / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Protein methylation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation at postsynapse / RMTs methylate histone arginines / A band / aminoacyl-tRNA synthetase multienzyme complex / translation at presynapse / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / 90S preribosome assembly / nucleolus organization / GAIT complex / TORC2 complex binding / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / cell-substrate adhesion / laminin receptor activity / homeostatic process / macrophage chemotaxis / lung morphogenesis / positive regulation of natural killer cell proliferation / basement membrane / fibroblast growth factor binding / monocyte chemotaxis / TOR signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / ubiquitin ligase inhibitor activity / 90S preribosome / ribonucleoprotein complex binding / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / regulation of translational fidelity / maturation of LSU-rRNA / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / Notch signaling pathway / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rough endoplasmic reticulum / positive regulation of cell cycle / laminin binding / ribosomal small subunit export from nucleus / gastrulation / translation initiation factor binding / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to interleukin-4
Similarity search - Function
40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : ...40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S19e, conserved site / : / Ribosomal protein S19e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L6e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 40S Ribosomal protein S10 / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S25 / : / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature.
Similarity search - Domain/homology
Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S6 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL33 ...Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / 40S ribosomal protein S6 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL33 / 60S ribosomal protein L41 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL22 / Ribosomal protein L37 / Large ribosomal subunit protein eL39 / 40S ribosomal protein S24 / 60S ribosomal protein L10 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL43 / 40S ribosomal protein S26 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS8 / 40S ribosomal protein S15 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL24 / Ribosomal protein L15 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL14 / 60S ribosomal protein L27 / Ribosomal protein L19 / Large ribosomal subunit protein uL15 / 60S ribosomal protein L36a / 60S ribosomal protein L32 / Large ribosomal subunit protein eL24 / 60S ribosomal protein L36 / Ubiquitin-ribosomal protein eL40 fusion protein / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL20 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 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 post-translocation non-rotated 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_55100.png

Downloads & links

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Map

FileDownload / File: emd_55100.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: 0.584
Minimum - Maximum-1.4835724 - 3.9555616
Average (Standard dev.)0.01776195 (±0.14657211)
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_55100_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_55100_half_map_2.map
Projections & Slices
AxesZYX

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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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 118185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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