Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome

Nature Structural & Molecular Biology volume 18, pages 715–720 (2011)Cite this article

Subjects

Abstract

No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34–Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the docking of crystal structures and homology models. Moreover, the close structural similarity of Dom34 and Hbs1 to eukaryotic release factors (eRFs) enabled us to propose a model for the ribosome-bound eRF1–eRF3 complex. Collectively, our data provide structural insights into how stalled mRNA is recognized on the ribosome and how the eRF complex can simultaneously recognize stop codons and catalyze peptide release.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The Dom34–Hbs1 complex bound to stem-loop stalled RNCs.
Figure 2: Interaction surface and conformational rearrangements of the Dom34–Hbs1 complex.
Figure 3: Destabilization of mRNA by the Dom34 NTD in the ribosomal decoding center.
Figure 4: Homology models for ribosome-bound eRF1–eRF3 complex.

Similar content being viewed by others

Accession codes

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Conti, E. & Izaurralde, E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17, 316–325 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Frischmeyer, P.A. et al. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295, 2258–2261 (2002).

    Article  CAS  PubMed  Google Scholar 

  3. van Hoof, A., Frischmeyer, P.A., Dietz, H.C. & Parker, R. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295, 2262–2264 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Doma, M.K. & Parker, R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440, 561–564 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lee, H.H. et al. Structural and functional insights into Dom34, a key component of no-go mRNA decay. Mol. Cell 27, 938–950 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Graille, M., Chaillet, M. & van Tilbeurgh, H. Structure of yeast Dom34: a protein related to translation termination factor eRF1 and involved in No-Go decay. J. Biol. Chem. 283, 7145–7154 (2008).

    Article  CAS  PubMed  Google Scholar 

  7. Chavatte, L., Seit-Nebi, A., Dubovaya, V. & Favre, A. The invariant uridine of stop codons contacts the conserved NIKSR loop of human eRF1 in the ribosome. EMBO J. 21, 5302–5311 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Frolova, L., Seit-Nebi, A. & Kisselev, L. Highly conserved NIKS tetrapeptide is functionally essential in eukaryotic translation termination factor eRF1. RNA 8, 129–136 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Passos, D.O. et al. Analysis of Dom34 and its function in no-go decay. Mol. Biol. Cell 20, 3025–3032 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Inagaki, Y. & Ford Doolittle, W. Evolution of the eukaryotic translation termination system: origins of release factors. Mol. Biol. Evol. 17, 882–889 (2000).

    Article  CAS  PubMed  Google Scholar 

  11. Carr-Schmid, A., Pfund, C., Craig, E.A. & Kinzy, T.G. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol. Cell. Biol. 22, 2564–2574 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Shoemaker, C.J., Eyler, D.E. & Green, R. Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop off to initiate no-go decay. Science 330, 369–372 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Beckmann, R. et al. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361–372 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. Hosoda, N. et al. Translation termination factor eRF3 mediates mRNA decay through the regulation of deadenylation. J. Biol. Chem. 278, 38287–38291 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Halic, M. et al. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427, 808–814 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Spahn, C.M. et al. Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell 107, 373–386 (2001).

    Article  CAS  PubMed  Google Scholar 

  17. Ben-Shem, A., Jenner, L., Yusupova, G. & Yusupov, M. Crystal structure of the eukaryotic ribosome. Science 330, 1203–1209 (2010).

    Article  CAS  PubMed  Google Scholar 

  18. Armache, J.P. et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution. Proc. Natl. Acad. Sci. USA 107, 19748–19753 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Armache, J.P. et al. Localization of eukaryote-specific ribosomal proteins in a 5.5-A cryo-EM map of the 80S eukaryotic ribosome. Proc. Natl. Acad. Sci. USA 107, 19754–19759 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Chen, L. et al. Structure of the Dom34–Hbs1 complex and implications for no-go decay. Nat. Struct. Mol. Biol. 17, 1233–1240 (2010).

    Article  CAS  PubMed  Google Scholar 

  21. Kobayashi, K. et al. Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex. Proc. Natl. Acad. Sci. USA 107, 17575–17579 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cheng, Z. et al. Structural insights into eRF3 and stop codon recognition by eRF1. Genes Dev. 23, 1106–1118 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kong, C. et al. Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. Mol. Cell 14, 233–245 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Song, H. et al. The crystal structure of human eukaryotic release factor eRF1–mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 100, 311–321 (2000).

    Article  CAS  PubMed  Google Scholar 

  25. Rabl, J., Leibundgut, M., Ataide, S.F., Haag, A. & Ban, N. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331, 730–736 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Gomez-Lorenzo, M.G. et al. Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 Å resolution. EMBO J. 19, 2710–2718 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Spahn, C.M. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23, 1008–1019 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Schuette, J.C. et al. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 28, 755–765 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Villa, E. et al. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc. Natl. Acad. Sci. USA 106, 1063–1068 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Schmeing, T.M. et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326, 688–694 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G. & Nyborg, J. Crystal structures of nucleotide exchange intermediates in the eEF1A–eEF1Bα complex. Nat. Struct. Biol. 8, 531–534 (2001).

    Article  CAS  PubMed  Google Scholar 

  32. Frolova, L. et al. Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA 2, 334–341 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Jenner, L.B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat. Struct. Mol. Biol. 17, 555–560 (2010).

    Article  CAS  PubMed  Google Scholar 

  34. Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).

    Article  CAS  PubMed  Google Scholar 

  35. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. The path of messenger RNA through the ribosome. Cell 106, 233–241 (2001).

    Article  CAS  PubMed  Google Scholar 

  36. Jenner, L.B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat. Struct. Mol. Biol. 17, 555–560 (2010).

    Article  CAS  PubMed  Google Scholar 

  37. Becker, T. et al. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science 326, 1369–1373 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Rawat, U. et al. Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. J. Mol. Biol. 357, 1144–1153 (2006).

    Article  CAS  PubMed  Google Scholar 

  39. Klaholz, B.P. et al. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421, 90–94 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Korostelev, A. et al. Crystal structure of a translation termination complex formed with release factor RF2. Proc. Natl. Acad. Sci. USA 105, 19684–19689 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Weixlbaumer, A. et al. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322, 953–956 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Church, G.M. & Gilbert, W. Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–1995 (1984).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Wagenknecht, T., Grassucci, R. & Frank, J. Electron microscopy and computer image averaging of ice-embedded large ribosomal subunits from Escherichia coli. J. Mol. Biol. 199, 137–147 (1988).

    Article  CAS  PubMed  Google Scholar 

  44. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).

    Article  CAS  PubMed  Google Scholar 

  45. Mindell, J.A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003).

    Article  PubMed  Google Scholar 

  46. Chen, J.Z. & Grigorieff, N. SIGNATURE: a single-particle selection system for molecular electron microscopy. J. Struct. Biol. 157, 168–173 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. Söding, J., Biegert, A. & Lupas, A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Eswar, N., Eramian, D., Webb, B., Shen, M.Y. & Sali, A. Protein structure modeling with MODELLER. Methods Mol. Biol. 426, 145–159 (2008).

    Article  CAS  PubMed  Google Scholar 

  49. Trabuco, L.G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank J. Musial for assistance in cloning, C. Ungewickell and J. Bürger (UltraStrukturNetzwerk Berlin) for assistance in cryo-EM data collection, S.W. Suh (Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea) for the gift of Dom34 and Hbs1 overexpression plasmids, K. Häussermann for assistance in cryo-EM data processing and D. Wilson for scientific discussions. This research was supported by grants from the Deutsche Forschungsgemeinschaft SFB594 and SFB646 (to R.B. and T.B.), SFB740 (to T.M.), by a Marie Curie international incoming fellowship within the Seventh European Community Framework Programme (to E.V.) and by the European Union and Senatsverwaltung für Wissenschaft, Forschung und Kultur Berlin (UltraStructureNetwork, Anwenderzentrum).

Author information

Authors and Affiliations

  1. Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany

    Thomas Becker, Jean-Paul Armache, Alexander Jarasch, Andreas M Anger, Heidemarie Sieber, Basma Abdel Motaal, Otto Berninghausen & Roland Beckmann

  2. Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Elizabeth Villa

  3. UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany

    Thorsten Mielke

  4. Institut für Medizinische Physik und Biophysik, Charité–Universitätsmedizin, Berlin, Germany

    Thorsten Mielke

Authors
  1. Thomas Becker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-Paul Armache
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alexander Jarasch
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andreas M Anger
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Elizabeth Villa
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Heidemarie Sieber
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Basma Abdel Motaal
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Thorsten Mielke
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Otto Berninghausen
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Roland Beckmann
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

T.B. collected, processed and analyzed all cryo-EM data and carried out docking and molecular interpretation; J.-P.A. provided models for S. cerevisiae ribosomal proteins; A.J. and A.M.A. provided models for S. cerevisiae ribosomal RNA; E.V. helped carry out molecular dynamics flexible fitting; H.S. did protein and RNC purifications, binding assays and northern blots; and B.A.M. cloned and purified the ΔN-Hbs1 protein. T.M. and O.B. assisted in cryo-EM data collection. T.B. and R.B. designed the study, analyzed data and wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Thomas Becker or Roland Beckmann.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, Supplementary Methods and Supplementary Tables 1–5 (PDF 4713 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Becker, T., Armache, JP., Jarasch, A. et al. Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome. Nat Struct Mol Biol 18, 715–720 (2011). https://doi.org/10.1038/nsmb.2057

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2057

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing