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

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.

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Figure 1: The crystal structure of a yeast exosome–RNA complex.
Figure 2: Interaction between Exo-9 and Rrp6.
Figure 3: Conformational rearrangements of Rrp44.
Figure 4: The RNA path through the exosome.
Figure 5: RNA channelling to degradation is a conserved mechanism.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited at the Protein Data Bank under accession number 4IFD.

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Acknowledgements

We would like to thank the Max Planck Institute Biochemistry Core Facility and Crystallization Facility; the staff members at beamlines X10SA (Swiss Light Source) and ID23-2 (European Synchrotron Radiation Facility) for support; F. Bonneau for the assay in Supplementary Fig. 6; J. Ebert, J. Basquin and F. Bonneau for initial materials and reagents; and P. Birle and T. Krywcun for technical assistance. We also thank members of our laboratory for discussions and critical reading of the manuscript. This study was supported by the Max Planck Gesellschaft, the ERC Advanced Investigator Grant 294371 and the Deutsche Forschungsgemeinschaft (SFB646, SFB1035, GRK1721 and CIPSM) to E.C.

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D.L.M. and E.C. designed the experiments. M.B. purified several exosome components. D.L.M. performed all other experiments and solved the structure. D.L.M. and E.C. wrote the manuscript.

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Correspondence to Elena Conti.

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The authors declare no competing financial interests.

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Makino, D., Baumgärtner, M. & Conti, E. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature 495, 70–75 (2013). https://doi.org/10.1038/nature11870

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