Fig. 4: Cryo-EM structural analysis of AUA decoding by ava2C34.
From: A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis
a, Atomic model of the E. coli 70S ribosome bound with mRNA (gray) and P. putida tRNAsIle2 at the P-site (blue) and A-site (green). b, Base pairing geometry of ava2C34 recognizing A3 of the AUA codon. The cryo-EM map (contoured at level 0.0277) is superimposed on the atomic models. c, Comparison of base pairing geometries between C34–G3 (orange, PDB ID: 4V5R)39 and ava2C34–A3 (green). The cytosine of ava2C34 moves to its minor groove by 2.9 Å compared with the C34–G3 pair. d, Model structures of ava2C34 recognizing the AUA codon in the decoding center of the A-site. Potential hydrogen bonds and the distances are indicated by dotted lines and red text, respectively. e, Chemical structures of ava2C34 recognizing the AUA codon facilitated by the hydrogen bond between the amide group of ava2C and 2′-OH of the mRNA residue 3′-adjacent to the AUA codon. The carbonyl oxygen of ava2C forms a hydrogen bond with 2′-OH of N4 residue in this model. Potential hydrogen bonds are shown by dotted lines. f, Structural comparison of ava2C34–A3 (green) and L34–A3 (blue) pairs at the A-site. Rotation and movement of U4 in mRNA and A1196 in 16S rRNA between these two structures are illustrated by arrows. Hydrogen bonds are shown by dotted lines.
