... Modeling the tmRNA structure in the ribosome . For modeling of the tmRNA-2 structure in the ribosome we used the published ribosome X-ray structure with a defined mRNA path (Yusupova et al, 2006). ... To model the initiation complex with the acceptor arm of TLD at the A-site and tRNA bound to the previous mRNA at the A-site, we used the X-ray structure of the ribosome with tRNAs bound to A- and P-site. ... The same approach was applied to create a model for tmRNA-4 in the ribosome (Fig. ...