Decoding site complex

Kondo, J. Fran9ois, B. Urzhumtsev, A. Westhof, E. Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin. Angew. Chem. Int. Ed. Engl. 2006, 45, 3310-3314. 

The Decoding On State of the Prokaryotic A-Site Complexed with... 

Accurate selection of translation termination factors to ribosomes containing a stop codon in the A-site is less well understood. A picture is only beginning to emerge as the bacterial 708 ribosome and class I release factor RF2 atomic models have recently been fitted into cryo-EM stmctures. Via multiple interactions RF2 connects the ribosomal decoding site with the PTC and functionally mimics a tRNA molecule in the A-site. In the complex RF2 is close to helices 18, 44, and 31 of the 168 rRNA, small subunit ribosomal protein 812, helices 69, 71, 89, and 92 of the 238 rRNA, the L7/L12 stalk, and protein LI 1 of the large subunit (Arkov et al. 2000 Klaholz et al. 2003 Rawat et al. 2003). The L7/L12 stalk inter-... 

As shown for streptomycin, the aminoglycosides bind at the 30 S subunit of the ribosome. The formation of the initiation complex is not inhibited. The translocation of the formylmethionine or peptidyl>t-RNA from the acceptor to the peptidyl site is disturbed. The bound t-RNA shifts the ribosome during the translocation from the decoding site to the condensing site and no more aminoacyl-t-RNA is bound. 

S. R. Lynch, R. L. Gonzalez, and J. D. Puglisi, Comparison of X-ray crystal structure of the 30s subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure, 11 (2003) 43-53. 

Macromolecular models should have a level of resolution commensurate with the quality and quantity of available data. We have developed a package of programs for building and refining models of nucleic acids and protein-nucleic acid complexes, with different levels of detail in different parts of the molecule. The method incorporates data from a variety of experiments. Our RNA models have atomic detail in some regions and lower resolution (typically one pseudoatom per nucleotide) in others. We are using this approach to refine models for the 308 subunit of the E. coli ribosome, with emphasis on the decoding site, where the 168 rRNA holds the mRNA and two tRNAs. 

We decided to model the decoding site using a combination of manual methods and MC-SYM (16-17). The models produced by MC-SYM incorporate base pairings, both canonical and non-canonical, along with information from probing experiments. Our model of the mRNA/tRNA complex (15) can be used as a starting point, if we can... 

There are two sets of key interactions between the decoding site and the mRNA/tRNA complex that allow us to enter into detailed modeling at atomic resolution. 

STRUCTURAL COMPARISONS BETWEEN PROKARYOTIC AND EUKARYOTIC RIBOSOMAL DECODING A SITES FREE AND COMPLEXED WITH AMINOGLYCOSIDES... 

Vicens, Q. Westhof, E. Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem. Biol. 2002, 9, 747-755. 

Codon-specific binding of an aminoacyl-tRNA (decoding). The binding of an aminoacyl-tRNA to the A site of the 70S or 80S initiation complex depends upon a protein called elongation factor Tu (EF-Tu... 

---