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. 2020 Oct 5;9:e51898. doi: 10.7554/eLife.51898

Figure 1. The ability of ASLPro to +1 frameshift in the peptidyl (P) site is dependent on the near-cognate mRNA codon.

(A) Secondary structure of the anticodon stem-loop (ASL) of tRNAPro. The m1G37 modified nucleotide is shown in orange and the anticodon nucleotides (C34, G35, and G36) and the U32-A38 pairing are labeled. (B) Structure of 70S-ASLPro bound to a cognate CCG codon in the P site with the codon in the 0 or canonical frame. All 2Fo-Fc electron density maps shown in panels B-D are contoured at 1.0σ. (C,D) Structure of 70S-ASLPro bound to a +1 slippery CCC-U codon shows the mRNA position is either in the 0 (panel C) or +1 frame (panel D) in the two 70S molecules in the crystallographic asymmetric unit. In either the 0 or +1 frame, a cis Watson–Crick interaction at the third base-pair forms (C+3•C34 or U+4•C34). mRNA numbering starts at +1 according to the first position in the P site.

Figure 1.

Figure 1—figure supplement 1. Determining the mRNA frame by visualizing the +4 nucleotide mRNA phosphate density.

Figure 1—figure supplement 1.

(A) A cognate G+3-C34 base-pair (mRNA nucleotide:anticodon nucleotide) is shown above. Representative 2Fo-Fc density is shown for the same cognate base-pairingbetween mRNA and ASLPro/tRNAPro(below). The phosphate of G+4is circled in red and its presence signifies that the mRNA is in the 0 frame (B) A near-cognate ASLPro C+3-C34 base-pair is shown with 2Fo-Fc density. The phosphate of U+4 is circled in red and its presence signifies that the mRNA is in the 0 frame. (C) A near-cognate ASLPro U+3-C34 base-pairi is shown with 2Fo-Fc density surrounding U+4.There is a lack of density for an addition phosphate group (circled in red) indicating that another nucleotide is not present and the mRNA is in the +1 frame. (D) A near-cognate tRNAPro C+3-C34 base-pair is shown with 2Fo-Fc density surrounding C+3.The phosphate of U+4 is circled in red and its presence signifies that the mRNA is in the 0 frame. 2Fo-Fc density are set at 1σ for all structures. The cutoff for a base-pair hydrogen bond is 3.5 Å.