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Structural insights into cognate versus near-cognate discrimination during decoding

Structural Biology Unit, CIC-bioGUNE, Derio, Basque Country, Spain.
The EMBO Journal (Impact Factor: 10.75). 03/2011; 30(8):1497-507. DOI: 10.1038/emboj.2011.58
Source: PubMed

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 ∼8% 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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Available from: Eduard Schreiner, Jul 28, 2015
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    • "Thus a molecular spring like mechanism is deciphered by the cryo-EM study during the tRNA selection and accommodation process. Furthermore, a very recent cryo-EM study (Agirrezabala et al. 2011 ) based on the analyses of the 70S⋅TC complexes containing a near-cognate aa-tRNA, in addition to its cognate counterpart, observed distinct structural changes, which indicates an induced fi t mechanism during aa-tRNA incorporation. The atomic details of some of the above fi ndings have been con fi rmed by the crystal structures of different 70S⋅TC complexes (Schmeing et al. 2009 ; Voorhees et al. 2010 ) . "
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