4V6K

Structural insights into cognate vs. near-cognate discrimination during decoding.

This is a non-PDB format compatible entry.

Summary for 4V6K

• Entry DOI: 10.2210/pdb4v6k/pdb
• EMDB information: 1849
• Descriptor: ribosomal RNA 5S, 50S ribosomal protein L11, 50S ribosomal protein L13, ... (57 entities in total)
• Functional Keywords: translation, ribosome, ternary complex, trna incorporation, cryoem, near-cognate
• Biological source: Escherichia coli; More
• Total number of polymer chains: 58
• Total formula weight: 2280361.06

Authors

Agirrezabala, X.,Schreiner, E.,Trabuco, L.G.,Lei, J.,Ortiz-Meoz, R.F.,Schulten, K.,Green, R.,Frank, J. (deposition date: 2011-01-07, release date: 2014-07-09, Last modification date: 2025-03-19)

Primary citation

Agirrezabala, X.,Schreiner, E.,Trabuco, L.G.,Lei, J.,Ortiz-Meoz, R.F.,Schulten, K.,Green, R.,Frank, J.
Structural insights into cognate versus near-cognate discrimination during decoding.
Embo J., 30:1497-1507, 2011

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.

PubMed: 21378755
DOI: 10.1038/emboj.2011.58

Experimental method

ELECTRON MICROSCOPY (8.25 Å)