Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods
Figure 3
(a) Cryo-EM reconstituted map of pseudoknot-stalled mammalian 40S small ribosomal subunit. The close-up view on the left shows the pseudoknot (PK, purple) binding to the putative ribosomal helicase site, namely, rpS3 (equivalent to prokaryotic S3), rpS9 (S4 in prokaryotes), and rpS2 (S5 in prokaryotes). Compared with the vacant 80S ribosome map (80SApo, green mesh), these subunits lining the mRNA entrance tunnel (yellow) move slightly toward the pseudoknot. The close-up view on the right shows pseudoknot-stalled P-site tRNA (tRNAPK) distortion relative to the stem-loop-stalled tRNA (tRNASL). The data implies that although both pseudoknot and stem-loop promote ribosome stalling, only pseudoknot can induce conformational changes in the ribosome complex. Figure reproduced with permission from [44]. (b) Close-up view of prokaryotic mRNA entrance tunnel [45] (PDB 3KNJ). Viewed from interior of the ribosome, residues implicated in interacting with the mRNA by ENM are labeled [46], and shown in ball-and-stick representations. Asterisks denote functional residues reported to be involved in ribosomal helicase activity (residues in S3 and S4) and translational fidelity (loop 2 in S5) by previous experiments [29, 47]. The ribosome reads mRNA in a 5′ to 3′ fashion, that is, opposite to mRNA movement indicated by the black arrow. Messenger RNA, S3, S4, and S5 are shown in orange, red, green, and blue, respectively.
