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

doi:10.1038/emboj.2011.58

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

Howard Hughes Medical Institution

Research output: Contribution to journal › Article › peer-review

44 Scopus citations

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 language	English (US)
Pages (from-to)	1497-1507
Number of pages	11
Journal	EMBO Journal
Volume	30
Issue number	8
DOIs	https://doi.org/10.1038/emboj.2011.58
State	Published - Apr 20 2011

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)

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10.1038/emboj.2011.58

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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.",

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AU - Trabuco, Leonardo G.

AU - Lei, Jianlin

AU - Ortiz-Meoz, Rodrigo F.

AU - Schulten, Klaus

AU - Green, Rachel

AU - Frank, Joachim

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Structural insights into cognate versus near-cognate discrimination during decoding

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Keywords

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