Fig. 6

Structural analysis of decoding modulation mediated by Q-glycosylation (A) Cryo-EM structure of the codon-anticodon interaction at the A-site of human 80S ribosome with human tRNAAsp bearing Q34 (green) and GAU codon (magenta) (PDB: 8JDJ ). 18S rRNA is colored cyan. H-bonds are shown as dotted lines. (B) Sphere representations of the codon-anticodon interaction (Q34 and GAU codon) viewed from the second base pair (left) and the first base pair (right). The van der Waals radius of the base atom is depicted in sphere representation (PDB: 8JDJ ). (C, E, and G) Cryo-EM structures of the codon-anticodon interaction at the A-site of human 80S ribosome with human tRNAAsp bearing Q34 (green) and GAU codon (magenta) (PDB: 8JDJ ) (C), human tRNAAsp bearing manQ34 (green) and GAU codon (magenta)(PDB: 8JDK) (E), and human tRNATyr bearing galQ34 (green) and UAU codon (magenta) (PDB: 8JDM ) (G), viewed from the major groove side. H-bonds are shown as dotted lines. (D) Structural alteration between Q34-C3 and Q34-U3 pairs. The Q34-C3 pair is superimposed on Q34-U3 by aligning C3 and U3. N2 and N10 of Q34 are shifted by 1.9 Å. The cyclopentene moiety of Q34 moves away from the major groove of the codon-anticodon helix. (F and H) Rotation of the cyclopentene moiety caused by glycosylation of Q34. Q34 (PDB: 8JDJ ) is aligned with manQ34 (PDB: 8JDK) (F) or galQ34 (PDB: 8JDM ) (H). Compared with Q34, the cyclopentene moieties of manQ34 and galQ34 are rotated by 160° and 170° in clockwise direction, respectively. See also Figures S4, S5, S6, S7, and S8 and Table S2.