Fig. 2: The Cm-binding site in the PTC is shaped by 23S rRNA, ions and the nascent peptide.

a, A composite in-cell ribosome map resolves mRNA, tRNAs and the native nascent peptide. Differently sharpened and blurred maps were combined to visualize the nascent peptide density (blue gray) from the PTC to the peptide exit site. b, Zoomed-in view for the nascent peptide density from the PTC to the exit site. c, Atomic model for mRNA (purple), A-site and P-site tRNAs (green and blue, respectively), nascent peptide (blue gray) and Cm (orange). The solid rectangle denotes the codon–anticodon pairing in the decoding center. The dashed rectangle denotes the Cm-binding site, described at higher detail in d–f. d, The Cm-binding pocket in the A-site of the PTC is formed by 23S rRNA nucleotides (cyan; only a few bases are displayed) and the nascent peptide (blue gray). For clarity, only positions 0 to −7 of the nascent peptide are shown. The first four residues (Asp-Ala-Ala-Lys) were modeled in accordance to a ribosome profiling study⁷. Density (purple) near the Cm-binding site was resolved and modeled as a K⁺ ion on the basis of previous studies^30,37. The CCA tail of aa-tRNA in the A-site (green) is shown with the corresponding density in d and f. e, Side view of the Cm-binding pocket. f, Top view of the binding pocket.