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- EMDB-39963: Cryo-EM structure of the human ubiquitylated 40S ribosome with RI... -

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Basic information

Entry
Database: EMDB / ID: EMD-39963
TitleCryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 (state Deg3)
Map dataconsensus map
Sample
  • Complex: ubiquitylated pre-40S ribosome with RIOK3
Keywordsubiquitylation / ribosome / RIOK3
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsHuang Z / Wang M / Li Y / Beckmann R / Cheng J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2025
Title: RIOK3 mediates the degradation of 40S ribosomes.
Authors: Zixuan Huang / Frances F Diehl / Mengjiao Wang / Yi Li / Aixia Song / Fei Xavier Chen / Nicolle A Rosa-Mercado / Roland Beckmann / Rachel Green / Jingdong Cheng /
Abstract: Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation ...Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3' end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis.
History
DepositionMay 1, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39963.png

Downloads & links

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Map

FileDownload / File: emd_39963.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 383.04 Å		1.06 Å/pix.
x 360 pix.
= 383.04 Å		1.06 Å/pix.
x 360 pix.
= 383.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.007655677 - 0.039862562
Average (Standard dev.)0.00018327696 (±0.0021644775)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local resolution filtered map

Fileemd_39963_additional_1.map
Annotationlocal resolution filtered map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_39963_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39963_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : ubiquitylated pre-40S ribosome with RIOK3

EntireName: ubiquitylated pre-40S ribosome with RIOK3
Components
  • Complex: ubiquitylated pre-40S ribosome with RIOK3

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Supramolecule #1: ubiquitylated pre-40S ribosome with RIOK3

SupramoleculeName: ubiquitylated pre-40S ribosome with RIOK3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#37
Source (natural)Organism: Homo sapiens (human)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4351

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23129
Initial angle assignmentType: OTHER / Details: Relion
Final angle assignmentType: OTHER / Details: Relion
FSC plot (resolution estimation)

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