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Structure of an Rrp6–RNA exosome complex bound to poly(A) RNA

Nature volume 511, pages 435439 (24 July 2014) | Download Citation

Abstract

The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3′ to 5′ exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3′ end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors are deposited in the Protein Data Bank with accession code 4OO1.

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Acknowledgements

We thank NE-CAT beamlines (Advanced Photon Source) supported by P41GM103403 (NIH NIGMS). APS is supported by the US Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. Beamline X29 (National Synchrotron Light Source) supported by the US Department of Energy, the Office of Basic Energy Sciences and P41RR012408 (NIH NCRR) and P41GM103473 (NIH NIGMS). Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award numbers F31GM097910 (E.V.W.) and R01GM079196 (C.D.L.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. C.D.L. is an investigator of the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Structural Biology Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10065, USA

    • Elizabeth V. Wasmuth
    • , Kurt Januszyk
    •  & Christopher D. Lima
  2. Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA

    • Elizabeth V. Wasmuth
  3. Howard Hughes Medical Institute, 1275 York Avenue, New York, New York 10065, USA

    • Christopher D. Lima

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Contributions

E.V.W. and C.D.L. designed and E.V.W. performed experiments for the S. cerevisiae exosomes. E.V.W. and C.D.L. determined the structure. K.J. and C.D.L. designed and K.J. performed the experiments for the Homo sapiens exosome. E.V.W. and C.D.L. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christopher D. Lima.

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https://doi.org/10.1038/nature13406

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