Fig. 6: Possible models in which each antibiotic that binds to 16S rRNA inhibits the binding of specific ribosome rescue factors to the empty A site of a ribosome.

A Left: Close-up views of superimposition of 16S rRNA of the small ribosomal subunit (PDB ID: 4V4Q) (green) and that bound with Par (4V5Y) (yellow). The backbone trace of 16S rRNA is depicted in either color; only A₁₄₉₂ and A₁₄₉₃ nucleotides in helix 44 are presented. A red arrow indicates changes in the base orientation caused by the Par binding. Middle and Right: Close-up views of superimposition of 16S rRNA bound with Par (4V5Y) and that with ArfB (6YSU) (middle) and that of 16S rRNA bound with Par and that with ArfA (5H5U) (right). van der Waals surfaces are presented for the bases of A₁₄₉₂ and A₁₄₉₃. The ribbon representations of ArfB and ArfA are depicted in red. Locations of putative clashes are surrounded by dotted skeleton boxes. Additionally, positions of putative clashed amino acid residues are indicated. All PDB data used in this Figure are from E. coli with the exception of 4DR3 (Str) from Thermus thermophiles. PyMOL (PyMOL Molecular Graphics System, Version 2.0, Schrödinger, LLC) was used to visualize and analyze all structures. B Left: Close-up views of superimposition of 16S rRNA (4V4Q) (green) and that bound with of Str (4DR3) (yellow). Only A₁₄₉₂ and A₁₄₉₃ nucleotides in the Str-bound 16S rRNA are indicated by black lines. A red arrow indicates a shift of the backbone of helix 44 laterally in the direction of ribosomal protein S12 and helix 18. Middle and Right: Close-up views of superimposition of 16S rRNA bound with Str (4DR3) and that with ArfB (6YSU) (middle) and that of 16S rRNA bound with Str and that with ArfA (5H5U) (right). C Left: Close-up views of the interaction between 16S rRNA and Tet (5J5B). Tet stacks with C₁₀₅₄ that is involved in decoding. The gray balls indicate Mg²⁺. The black and purple dashed lines indicate hydrogen bonds and electrical interactions, respectively. Middle: Close-up view of the superimposed small subunits structures focusing on the Tet-binding (5J5B), the SmpB-binding (7AC7), and the tRNA/mRNA binding (4V66). tRNA and mRNA are depicted in warmpink and salmon, respectively. A van der Waals surface is presented for Tet. Right, Top: Putative clash between Tet (5J5B) and the first nucleotide of anticodon (G₃₄) in tRNA (4V66). Right, bottom: Putative clashes between Lys134 in SmpB (7AC7) and Tet (5J5B) and between Lys134 and C₁₀₅₄ in 16S rRNA (5J5B). van der Waals surfaces are presented for G₃₄ and Lys134.