Fig. 3: Structural details of the nascent chain in the nonrotated state and effects of mutations in the NC.
From: Selective inhibition of human translation termination by a drug-like compound
a The CDH1–NPN nascent-chain model within the cryo-EM density (transparent surface). rRNA bases (light cyan) and ribosomal protein residues (light green for uL22 and pink for uL4) that have close interactions with the nascent chain are shown. The amino acids of the nascent chain found to be essential for PF846-mediated stalling are colored blue. Amino acids without numbers are I722, L725, N726, P727, and N728 at the C terminus. b Models of different amino acids at the NC C-terminal position 728. The pocket formed by 28S rRNA nucleotides A3887 and C3888 can accommodate different sizes of amino acid, with methionine (M728) and phenylalanine (F728) as examples. c, d Interactions between P727 and N726 with adjacent 28S rRNA nucleotides. Dashed lines indicate hydrogen bonds and spheres represent van der Waals radii of C, N, and O atoms. e Western blots of FLAG-tagged CDH1–NPN nascent chains containing single mutations, from in vitro translation reactions in the presence (+) or absence (−) of 50 μM PF846. The mutations that affect termination are indicated with asterisks. The positions of tRNA-bound and free nascent chains are shown, with RPLP0 serving as a loading control. f, i Interactions between 28S rRNA nucleotides and the PF846-stalled nascent chain in the nonrotated RNC with dashed lines indicating hydrogen bonds and spheres representing van der Waals radii. j–l Direct interactions between PF846 and nascent-chain residues. Spheres represent van der Waals radii. O, N, and Cl atoms are colored in red, blue, and green, respectively. The experiment shown in e was repeated three times independently with similar results.
