Fig. 2

AGs target the decoding center of the leishmanial cytosolic ribosome. a An overall view of the cryo-EM structure with three tRNAs at their designated locations at the A-, P-, and E-sites (pink) and mRNA (yellow). PAR is shown in cyan, rRNA in gray, and ribosomal proteins in green and light blue for the small and large subunits, respectively. b Close-up view of PAR in density map. Observed density is contoured around the ligand at 5.0 σ. c PAR interactome within its binding pocket at the leishmanial ribosome. PAR maintains a dense array of electrostatic interactions with RNA residues within the binding pocket at the SSU. Ring numbers (I–IV) for PAR and atom names are specified. rRNA atoms are numbered according to the Leishmania numbering (with E. coli numbering in parenthesis). Hydrogen bonds and salt bridges are presented as yellow dashed lines. Bond lengths are presented in black in ångström (Å). d The PAR-binding pocket in the leishmanial cytosolic ribosome corresponds to the AG target in bacterial ribosomes and is localized at the tip of h44 at the SSU decoding center. Similar to bacteria, PAR binding dictates the flipped-out conformation of two highly conserved adenine residues, A2158 and A2159, blue and red, respectively (A1492 and A1493 in E. coli numbering), resulting in interactions with both the mRNA A-site codon (yellow) and the A-site tRNA anticodon loop (magenta). Additional conserved elements within the binding pocket include the universally conserved protein uS12 (purple) G626 of h18 (G530 in E. coli numbering, gray) and Am502β of LSU H69 (A1913 in E. coli, light green). e The ribosomal proteins eS30 (lime) and eL41 (orange), which are of sole eukaryotic origin, penetrate the drug binding pocket and maintain close interactions with binding site surroundings. f The eukaryote conserved His5 of eS30 (lime) maintains electrostatic interactions with both universally conserved A2158 (blue) and ms²m⁶A37 of A-site tRNA anticodon loop (magenta). g, h Eukaryotic proteins in the binding pocket that could not be resolved in earlier published structures due to regional flexibility are shown in density. eL41 (g) highlighted in orange, and eS30 (h) in green. Densities are shown at 3.0 σ