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TitleRIOK3 mediates the degradation of 40S ribosomes.
Journal, issue, pagesMol Cell, Vol. 85, Issue 4, Page 802-814.e12, Year 2025
Publish dateFeb 20, 2025
AuthorsZixuan Huang / Frances F Diehl / Mengjiao Wang / Yi Li / Aixia Song / Fei Xavier Chen / Nicolle A Rosa-Mercado / Roland Beckmann / Rachel Green / Jingdong Cheng /
PubMed AbstractCells 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.
External linksMol Cell / PubMed:39947183
MethodsEM (single particle)
Resolution3.6 - 8.2 Å
Structure data

39956

8zdb

EMDB-39956, PDB-8zdb:
Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3
Method: EM (single particle) / Resolution: 3.6 Å

39957

8zdc

EMDB-39957, PDB-8zdc:
Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3
Method: EM (single particle) / Resolution: 3.8 Å

39958

8zdd

EMDB-39958, PDB-8zdd:
Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 (without NOB1)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-39959: Cryo-EM structure of the human ubiquitylated 40S ribosome dimer with RIOK3
Method: EM (single particle) / Resolution: 8.2 Å

EMDB-39960: Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 (state Deg1)
Method: EM (single particle) / Resolution: 4.8 Å

EMDB-39962: Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 (state Deg2)
Method: EM (single particle) / Resolution: 6.4 Å

EMDB-39963: Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 (state Deg3)
Method: EM (single particle) / Resolution: 4.9 Å

EMDB-39964: Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 (state Deg4)
Method: EM (single particle) / Resolution: 4.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
KeywordsRIBOSOME / ubiquitylation / RIOK3

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