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


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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. 1

    Lykke-Andersen, S., Brodersen, D. E. & Jensen, T. H. Origins and activities of the eukaryotic exosome. J. Cell Sci. 122, 1487–1494 (2009)

    CAS  Article  Google Scholar 

  2. 2

    Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763–776 (2009)

    CAS  Article  Google Scholar 

  3. 3

    Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M. & Tollervey, D. The exosome: A conserved eukaryotic RNA processing complex containing multiple 3′->5′ exoribonucleases. Cell 91, 457–466 (1997)

    CAS  Article  Google Scholar 

  4. 4

    Lorentzen, E. et al. The archeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Struct. Mol. Biol. 12, 575–581 (2005)

    CAS  ADS  Article  Google Scholar 

  5. 5

    Büttner, K., Wenig, K. & Hopfner, K.-P. Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol. Cell 20, 461–471 (2005)

    Article  Google Scholar 

  6. 6

    Liu, Q., Greimann, J. C. & Lima, C. D. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127, 1223–1237 (2006)

    CAS  Article  Google Scholar 

  7. 7

    Lorentzen, E. & Conti, E. Structural basis of 3′ end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol. Cell 20, 473–481 (2005)

    CAS  Article  Google Scholar 

  8. 8

    Navarro, M. V. A. S., Oliverira, C. C., Zanchin, N. I. T. & Guimarães, B. G. Insights into the mechanism of progressive RNA degradation by the archaeal exosome. J. Biol. Chem. 283, 14120–14131 (2008)

    CAS  Article  Google Scholar 

  9. 9

    Hardwick, S. W., Gubbey, T., Hug, I., Jenal, U. & Luisi, B. F. Crystal structure of Caulobacter crescentus polunucleotide phosphorylase reveals a mechanism of RNA substrate channelling and RNA degradosome assembly. Open Biol. 2, 120028 (2012)

    Article  Google Scholar 

  10. 10

    Dziembowski, A., Lorentzen, E., Conti, E. & Séraphin, B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nature Struct. Mol. Biol. 14, 15–22 (2007)

    CAS  Article  Google Scholar 

  11. 11

    Noguchi, E. et al. Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J. 15, 5595–5605 (1996)

    CAS  Article  Google Scholar 

  12. 12

    Allmang, C. et al. The yeast exosome and human PM-Scl are related complexes of 3′->5′ exonucleases. Genes Dev. 13, 2148–2158 (1999)

    CAS  Article  Google Scholar 

  13. 13

    Lorentzen, E., Basquin, J., Tomecki, R., Dziembowski, A. & Conti, E. Structure of the active subunit of the yeast exosome core, Rrp44: Diverse modes of substrate recruitment in the RNase II nuclease family. Mol. Cell 29, 717–728 (2008)

    CAS  Article  Google Scholar 

  14. 14

    Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E. & Conti, E. The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139, 547–559 (2009)

    CAS  Article  Google Scholar 

  15. 15

    Wasmuth, E. V. & Lima, C. D. Exo- and endoribonucleolytic activities of yeast cytoplasmic and nuclear RNA exosomes are dependent on the noncatalytic core and central channel. Mol. Cell 48, 133–144 (2012)

    CAS  Article  Google Scholar 

  16. 16

    Lebreton, A., Tomecki, R., Dziembowski, A. & Séraphin, B. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456, 993–996 (2008)

    CAS  ADS  Article  Google Scholar 

  17. 17

    Schaeffer, D. et al. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nature Struct. Mol. Biol. 16, 56–62 (2009)

    CAS  Article  Google Scholar 

  18. 18

    Schneider, C., Leung, E., Brown, J. & Tollervey, D. The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Nucleic Acids Res. 37, 1127–1140 (2009)

    CAS  Article  Google Scholar 

  19. 19

    Wang, H.-W. et al. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3′ end processing. Proc. Natl Acad. Sci. USA 104, 16844–16849 (2007)

    CAS  ADS  Article  Google Scholar 

  20. 20

    Malet, H. et al. RNA channelling by the eukaryotic exosome. EMBO Rep. 11, 936–942 (2010)

    CAS  Article  Google Scholar 

  21. 21

    Briggs, M. W., Burkard, K. T. & Butler, J. S. Rrp6, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8S rRNA 3′ end formation. J. Biol. Chem. 273, 13255–13263 (1998)

    CAS  Article  Google Scholar 

  22. 22

    Cristodero, M., Böttcher, B., Diepholz, M., Scheffzek, K. & Clayton, C. The Leishmania tarentolae exosome: purification and structural analysis by electron microscopy. Mol. Biochem. Parasitol. 159, 24–29 (2008)

    CAS  Article  Google Scholar 

  23. 23

    Callahan, K. P. & Butler, J. S. Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res. 36, 6645–6655 (2008)

    CAS  Article  Google Scholar 

  24. 24

    Lorentzen, E., Dziembowski, A., Lindner, D., Seraphin, B. & Conti, E. RNA channelling by the archaeal exosome. EMBO Rep. 8, 470–476 (2007)

    CAS  Article  Google Scholar 

  25. 25

    Frazão, C. et al. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 443, 110–114 (2006)

    ADS  Article  Google Scholar 

  26. 26

    Schneider, C., Kudla, G., Wlotzka, W., Tuck, A. & Tollervervey, D. Transcriptome-wide analysis of exosome targets. Mol. Cell 48, 422–433 (2012)

    CAS  Article  Google Scholar 

  27. 27

    Lupas, A., Flanagan, J. M., Tamura, T. & Baumeister, W. Self-compartmentalizing proteases. Trends Biochem. Sci. 22, 399–404 (1997)

    CAS  Article  Google Scholar 

  28. 28

    Greimann, J. C. & Lima, C. D. Reconstitution of RNA exosomes from human and Saccharomyces cerevisiae cloning, expression, purification, and activity assays. Methods Enzymol. 448, 185–210 (2008)

    CAS  Article  Google Scholar 

  29. 29

    Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH image to ImageJ: 24 years of image analysis. Nature Methods 9, 671–675 (2012)

    CAS  Article  Google Scholar 

  30. 30

    Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    CAS  Article  Google Scholar 

  31. 31

    Oddone, A. et al. Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep. 8, 63–69 (2007)

    CAS  Article  Google Scholar 

  32. 32

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

  33. 33

    Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D. 67, 235–242 (2011)

    CAS  Article  Google Scholar 

  34. 34

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  35. 35

    Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66,. 213–221 (2010)

  36. 36

    The PyMOL Molecular Graphics System. v. 1.2r3pre (Schrödinger, LLC).

  37. 37

    Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001)

    CAS  ADS  Article  Google Scholar 

  38. 38

    Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38, W529–W533 (2010)

    CAS  Article  Google Scholar 

  39. 39

    Reichmann, D. et al. Binding hot spots in the TEM1-BLIP interface in light of its modular architecture. J. Mol. Biol. 365, 663–679 (2007)

    CAS  Article  Google Scholar 

Download references


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.

Author information




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.

Corresponding author

Correspondence to Elena Conti.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-2, Supplementary Figures 1-6 and additional references. (PDF 5037 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.