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Structure paper

TitleStructural basis of mRNA decay by the human exosome-ribosome supercomplex.
Journal, issue, pagesNature, Vol. 635, Issue 8037, Page 237-242, Year 2024
Publish dateOct 9, 2024
AuthorsAlexander Kögel / Achim Keidel / Matina-Jasemi Loukeri / Christopher C Kuhn / Lukas M Langer / Ingmar B Schäfer / Elena Conti /
PubMed AbstractThe interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated ...The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. ). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.
External linksNature / PubMed:39385025 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 7.0 Å
Structure data

51132

9g8m

EMDB-51132, PDB-9g8m:
human 80S ribosome bound by a SKI2-exosome complex
Method: EM (single particle) / Resolution: 3.3 Å

51133

9g8n

EMDB-51133, PDB-9g8n:
80S-bound human Ski2-exosome complex
Method: EM (single particle) / Resolution: 3.7 Å

51134

9g8o

EMDB-51134, PDB-9g8o:
human 40S ribosome bound by a SKI238-exosome complex
Method: EM (single particle) / Resolution: 3.4 Å

51135

9g8p

EMDB-51135, PDB-9g8p:
40S-bound human SKI2-exosome complex
Method: EM (single particle) / Resolution: 7.0 Å

51136

9g8q

EMDB-51136, PDB-9g8q:
40S-bound human SKI238 complex in the open state (Gatekeeping module)
Method: EM (single particle) / Resolution: 4.1 Å

51137

9g8r

EMDB-51137, PDB-9g8r:
human SKI7-SKI238 complex in the open state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-51139: human 80S ribosome bound by a SKI2-exosome complex (60S signal subtracted)
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
  • cricket paralysis virus
KeywordsRIBOSOME / RNase / Helicase / RNA-binding / mRNA-degradation / cytoplasm / RNA-degradation / HYDROLASE

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