Structural insights into cognate versus near-cognate discrimination during decoding

Xabier Agirrezabala, Eduard Schreiner, Leonardo G. Trabuco, Jianlin Lei, Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, Joachim Frank

Research output: Contribution to journalArticle

Abstract

The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA Trp in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼48% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.

Original languageEnglish (US)
Pages (from-to)1497-1507
Number of pages11
JournalEMBO Journal
Volume30
Issue number8
DOIs
StatePublished - Apr 20 2011

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Keywords

  • cryo-EM
  • ribosome
  • tRNA incorporation
  • ternary complex
  • translation

ASJC Scopus subject areas

  • Neuroscience(all)
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Agirrezabala, X., Schreiner, E., Trabuco, L. G., Lei, J., Ortiz-Meoz, R. F., Schulten, K., Green, R., & Frank, J. (2011). Structural insights into cognate versus near-cognate discrimination during decoding. EMBO Journal, 30(8), 1497-1507. https://doi.org/10.1038/emboj.2011.58