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. 2014 Jun 9;111(25):9139–9144. doi: 10.1073/pnas.1406335111

Fig. 3.

Fig. 3.

Positioning of PKI in the decoding center of the ribosome is similar to that of the A-site tRNA and mRNA codon. (A) Comparison of the TSV IRES RNA (red) location on the 40S subunit (cyan) with tRNA positions in the A (yellow), P (blue), and E (gray) sites. Superposition was obtained by structural alignment of 16S ribosomal RNA from the crystal structure of a 70S•mRNA•tRNA complex containing three tRNAs (PDB ID code 3I8H) (29) with 18S ribosomal RNA of structure I (this work). (B) Comparison of PKI structure (red) with the mRNA (green) and tRNA (yellow) bound to the A site. (C) Structure of the decoding center of the 80S•TSV IRES complex fitted into the cryo-EM map (class I, gray mesh). PKI of the IRES RNA is shown in red, 18S rRNA is shown in cyan, 25S rRNA is shown in yellow-green, and ribosomal proteins are shown in blue. (D) Interactions of the anticodon stem loop of cognate tRNA (yellow) and mRNA (green) with the universally conserved elements of the decoding center in bacterial 70S ribosomes (29). The 16S rRNA is shown in cyan, and the 23S rRNA is shown in gray. (E) Interactions of PKI of the TSV IRES RNA with the decoding center of the 80S ribosome (this work), whose conformation resembles that of the tRNA-bound decoding center (D). Colors are as in C. A figure without mesh, showing the same view as in E, is presented in Fig. S4.