Fig. 4.
Interactions of e*/E tRNASufA6 with 16S rRNA. (A) tRNASufA6 binds in a newly defined e*/E site where the CCA end is located on the 50S E site and the ASL is closer to the 30S E site. The mRNA is numbered with +1 (yellow) corresponding to the 5′ nucleotide of the 4-nt frameshifting codon. The boxed region is shown in more detail in C. (B) Structure of 70·EF-G translocation intermediates state showing the tRNA located between the 30S P and the E sites, termed pe*/E (PDB ID code 4V9L). In this state, the +1 and +2 mRNA codon nucleotides (magenta) are in the E site, the +3 nucleotide is in the P site, and 16S rRNA nucleotide G926 is packed beneath. The dotted line signifies the boundary between the E and the P sites, and the black arrow denotes the 1-nt gap between G693 and the +1 nucleotide of the codon. 16S rRNA nucleotide A1503 is stably intercalated between the −1 and −2 nucleotides of the mRNA. (C) In the e*/E tRNASufA6 structure, the +1 mRNA nucleotide (yellow) is pulled into the E site and packs directly against G693. 16S rRNA nucleotide G926 also flanks the +3/+4 mRNA codon, but A1503 no longer stacks with mRNA nucleotides −1 and −2 (denoted by red arrows).