Fig. 3

The structure of PHZ in complex with the bacterial ribosome. a Cryo-EM map of PHZ in complex with the E. coli 70S ribosome (green mesh). The fitted model of the compound is displayed in its respective charge density viewed from two different perspectives. The map is contoured at 2.5σ. Carbon atoms are colored yellow, nitrogen atoms are blue, oxygen atoms are red, and sulfur atoms are green. b Schematic diagram showing that only residues 2–23 of the ribosome-bound PHZ molecule are visible in the cryo-EM map. c, d Overview of the PHZ-binding site (yellow) on the E. coli large ribosomal subunit (light blue) viewed from two different perspectives. In c, the 50S subunit is viewed from the inter-subunit interface (30S subunit is removed for clarity) as indicated by the inset. The view in d is from the cytoplasm onto the A site. e, f Close-up views of the PHZ-binding site in the ribosome exit tunnel. E. coli numbering of the nucleotides in the 23S rRNA is used. Potential H-bond interactions are indicated with dotted lines