Figure 4. Frame-dependent conformations of the mRNA in the E and P sites.
(A) Overview of the 70S ribosome with (B) a zoomed-in view of the mRNA-tRNA interaction in the A, P, and E sites (PDB code 4V6F). 16S rRNA nucleotides G693 and G926 interact with the E-site codon–anticodon. (C) The normal path of the mRNA (black) in a ribosome structure containing P/P and E/E tRNAs demonstrates only a three-nucleotide codon (nucleotides +1, +2 and +3) is accommodated in the E site (PDB code 4V5F). 16S rRNA G693 defines the starts of the E-site codon and interacts with the first nucleotide. As the mRNA leaves the E site, there is a 100° kink between the first nucleotide of the E-site codon (+1) and the −1 nucleotide (shaded in purple). Panel C is rotated ~180° relative to the view in panel B. (D) A translocation intermediate structure induced by EF-G contains a tRNA positioned between the P and the E sites on the 30S (denoted ‘pe’). The pe/E tRNA has not undergone full translocation to the E site and thus only two nucleotides (+1 and +2) are located in the E site (PDB code 4W29). In this translocation intermediate state, there is space available to accommodate an additional nucleotide of the codon (shaded in red) that would occur upon full translocation. (E) tRNAPro bound to a +1 slippery CCC-U codon reveals that although the codon–anticodon pair has not been fully translocated, this placement of the mRNA is different as compared to normal translocation intermediates structures as shown in panel D. The additional nucleotide (+4) of the four-nucleotide codon is shown in green.