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TitleConcerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.
Journal, issue, pagesMol Cell, Vol. 83, Issue 22, Page 4093-44105.e7, Year 2023
Publish dateNov 16, 2023
AuthorsAchim Keidel / Alexander Kögel / Peter Reichelt / Eva Kowalinski / Ingmar B Schäfer / Elena Conti /
PubMed AbstractThe Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the ...The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes.
External linksMol Cell / PubMed:37879335 / PubMed Central
MethodsEM (single particle)
Resolution2.55 - 3.12 Å
Structure data

EMDB-18288, PDB-8q9t:
CryoEM structure of a S. Cerevisiae Ski238 complex bound to RNA
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-18326, PDB-8qca:
CryoEM structure of a S. Cerevisiae Ski2387 complex in the closed state bound to RNA
Method: EM (single particle) / Resolution: 2.84 Å

EMDB-18327: CryoEM structure of a S. Cerevisiae Ski2387 complex in an intermediate state bound to RNA
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-18328, PDB-8qcb:
CryoEM structure of a S. Cerevisiae Ski2387 complex in the open state
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-18329, PDB-8qcf:
yeast cytoplasmic exosome-Ski2 complex degrading a RNA substrate
Method: EM (single particle) / Resolution: 2.55 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsHYDROLASE / Helicase / RNA binding / RNA degradation

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