Fig. 2: Structural characterization of U^p47 in S. tokodaii tRNA^Val3.

a, Overview of the crystal structures of S. tokodaii tRNA^Val3. Molecules A and B are shown in stick representation in white and light green, respectively. U^p47 is shown in red. The 2F_o–F_c electron density map contoured at 1.0σ around U^p47 is shown in the lower right box for each molecule. 2′p, 2′-phosphate. b, Close-up views of the core structures of molecules A (left) and B (right). U^p47 (red) and the top (15–48; black), second (8–14–21; green), third (13–22–46; blue), fourth (9–12–23; yellow), fifth (11–24; orange), sixth (10–25–45; pink) and seventh (26–44; light purple) layers are shown in stick representation. c, Schematic views of the core structures of molecules A (left) and B (right). d, f, g, Atomic structures of the base triples s⁴U8–A14–A21 (d), Ψ13–G22–G46 (f) and C12–G23–C9 (g) in the core region of molecules A (left) and B (right). Dashed lines indicate predicted interactions with bond length (Å). U^p47 is shown in red. e, The V-loop structures of molecule (mol.) A (blue), molecule B (green) and Saccharomyces cerevisiae tRNA^Phe (PDB, 1EHZ) (gold) are overlaid. The residues at position 47 are shown in stick representation. The 2′-phosphate of U^p47 is indicated. h, The V-loop structures of intact tRNA molecule A (blue), Tpt1p-treated tRNA molecule A (magenta) and Tpt1p-treated tRNA molecule B (orange) are overlaid. The residues at position 47 are shown in stick representation. The 2′-phosphate of U^p47 is indicated.