Skip to main content

Thank you for visiting 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.

  • Letter
  • Published:

Unusual base pairing during the decoding of a stop codon by the ribosome


During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine–purine base pairs1. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNASer bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine–purine base pairs at the second and third positions of the codon, which show an unusual Watson–Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.

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

Access options

Buy this article

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

Figure 1: Chemical differences between uridine and pseudouridine, and experimental set-up.
Figure 2: Overall and detailed view of the base pairs involved in the codon–anticodon interaction.
Figure 3: Interaction of ribosomal bases with the codon–anticodon base pairs.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and structure factors have been deposited in the PDB under accessions 4JV5, 4JYA, 4K0K (30S) and 4K0L, 4K0M, 4K0P, 4K0Q (70S).


  1. Karijolich, J. & Yu, Y.-T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395–398 (2011)

    Article  CAS  Google Scholar 

  2. Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001)

    Article  CAS  ADS  Google Scholar 

  3. Ogle, J. M., Murphy, F. V., Tarry, M. J. & Ramakrishnan, V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721–732 (2002)

    Article  CAS  Google Scholar 

  4. 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  ADS  Google Scholar 

  5. Voorhees, R. M., Schmeing, T. M., Kelley, A. C. & Ramakrishnan, V. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330, 835–838 (2010)

    Article  CAS  ADS  Google Scholar 

  6. Pape, T., Wintermeyer, W. & Rodnina, M. V. Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17, 7490–7497 (1998)

    Article  CAS  Google Scholar 

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

    Article  CAS  ADS  Google Scholar 

  8. Leontis, N. B. & Westhof, E. Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001)

    Article  CAS  Google Scholar 

  9. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. & Steinberg, S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26, 148–153 (1998)

    Article  CAS  Google Scholar 

  10. Nikolova, E. N. et al. Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470, 498–502 (2011)

    Article  CAS  ADS  Google Scholar 

  11. Davis, D. R., Veltri, C. A. & Nielsen, L. An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNALys, tRNAHis and tRNATyr. J. Biomol. Struct. Dyn. 15, 1121–1132 (1998)

    Article  CAS  Google Scholar 

  12. Yarian, C. S. et al. Structural and functional roles of the N1- and N3-protons of Ψ at tRNA’s position 39. Nucleic Acids Res. 27, 3543–3549 (1999)

    Article  CAS  Google Scholar 

  13. Tomita, K., Ueda, T. & Watanabe, K. The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res. 27, 1683–1689 (1999)

    Article  CAS  Google Scholar 

  14. Huang, C., Wu, G. & Yu, Y.-T. Inducing nonsense suppression by targeted pseudouridylation. Nature Protocols 7, 789–800 (2012)

    Article  CAS  Google Scholar 

  15. Winn, M. D., Murshudov, G. N. & Papiz, M. Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003)

    Article  CAS  Google Scholar 

  16. Borel, F., Hartlein, M. & Leberman, R. In vivo overexpression and purification of Escherichia coli tRNAser. FEBS Lett. 324, 162–166 (1993)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011)

    Article  CAS  Google Scholar 

  19. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  20. DeLano, W. L. The PyMOL Molecular Graphics System. (2006)

Download references


We thank D. Hall and G. Winter for help and advice with data collection at beamline I04, Diamond Light Source; T. Tomizaki at beamline X06SA for help with data collection at the Swiss Light Source; and A. McCarthy at beamline ID14-4, ESRF, where screening and initial data collection were done. We thank M. Härtlein for the gift of an overproducing tRNASer clone, M. Torrent for advice on yeast tRNA abundance, and G. Murshudov for advice and help with data analysis and refinement. V.R. was supported by the UK Medical Research Council (grant U105184332), a Programme Grant and Senior Investigator Award from the Wellcome Trust, the Agouron Institute and the Louis-Jeantet Foundation. Y.-T.Y. was supported by a grant from the National Institutes of Health (GM104077), and by the University of Rochester CTSA award (UL1TR000042) from the National Center for Advancing Translational Sciences of the National Institutes of Health. I.S.F. was supported by a postdoctoral fellowship from the Fundacion Ramon Areces.

Author information

Authors and Affiliations



I.S.F. carried out the crystallographic experiments and analysis and helped write the paper, G.W. did the in vitro translation assays, C.L.N. helped with crystallographic data collection, A.C.K. made the 30S subunits, 70S ribosome and tRNASer, and Y.-T.Y. and V.R. oversaw the project and helped write the paper.

Corresponding authors

Correspondence to Yi-Tao Yu or V. Ramakrishnan.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 and Supplementary Figures 1-2. (PDF 1076 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fernández, I., Ng, C., Kelley, A. et al. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature 500, 107–110 (2013).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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.


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