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Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex

Author

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  • Debora Lika Makino

    (MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany)

  • Marc Baumgärtner

    (MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany)

  • Elena Conti

    (MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany)

Abstract

The exosome is the major 3′–5′ RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3′-overhang of 31 ribonucleotides. The 2.8 Å resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3′-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3′–5′ RNA degradation complexes are conserved in all kingdoms of life.

Suggested Citation

  • Debora Lika Makino & Marc Baumgärtner & Elena Conti, 2013. "Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex," Nature, Nature, vol. 495(7439), pages 70-75, March.
    • Handle: RePEc:nat:nature:v:495:y:2013:i:7439:d:10.1038_nature11870
    DOI: 10.1038/nature11870
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    Cited by:

    1. Ewelina M. Małecka & Sarah A. Woodson, 2024. "RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Komal Soni & Anusree Sivadas & Attila Horvath & Nikolay Dobrev & Rippei Hayashi & Leo Kiss & Bernd Simon & Klemens Wild & Irmgard Sinning & Tamás Fischer, 2023. "Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

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