Extended Data Fig. 10: Structural characterization of the ava2C–A pair on the ribosome and its comparison with other cytidine modifications.
From: A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis
a, Codon–anticodon interactions at P- and A-sites of the 70S ribosome. mRNA kinks by ~45° between P- and A-site codons. ava2C–A pairs are visible and common at both sites, but the density of the ava2C side chains is seen only at the A-site. b, Model structures of ava2C34 (left), L34 (middle) and agm2C34 (right) recognizing the AUA codon in the decoding center of the A-site. Potential H-bonds and the distances are indicated by dotted lines and red text, respectively. c, Hypothetical ava2C34–G3 pairing in a canonical Watson–Crick geometry. The aminovaleramide group of ava2C34 clashes with N2-amine of G3. d, Solvent-excluded surface models showing the structural complementarity of the long side chains of ava2C34 (left), L34 (middle) and agm2C (right), and the cleft formed by rRNA residues and the mRNA strand at the A-site. A large area of van der Waals contacts between ava2C34 and rRNA residues, and the mRNA is clearly visible. e, Another possible hydrogen bonding pattern of ava2C34 and mRNA residues.
