Figure 4.

Schematic presentation of the Sgm–30S ribosomal subunit complex. (A) Summary of the footprinting results. Sections of the 16S rRNA that were analyzed by primer extension are shaded in grey. Nucleotides protected upon Sgm binding are indicated with a black dot, whereas exposed nucleotides are indicated with a black triangle symbol. For circle indicated regions, structural change was observed upon Sgm binding to 30S subunits. Helix numbering is presented in boxes. After chemical footprint, rRNA was extended with reverse transcriptase with primers complementary to regions: (1) 817–833, (2) 939–955 and (3) 1459–1479. (B) Mapping of footprinting data onto the 30S structure. Components of the 30S subunit are shown in the surface representation, ribosomal proteins are indicated in dark gray, 16S rRNA is indicated in light gray with the exception of helix 44 (residues 1400–1499), shown in white. Results of the footprinting experiments are color coded as follows: residues relatively more reactive in the footprinting experiment are shown in green, residues less reactive in the footprinting experiment are shown in red. The target G1405 is shown in yellow and is additionally indicated by a yellow circle. (C) Extreme steric clashes between Sgm and the 30S subunit occur, if the enzyme is docked to its target in helix 44 without any conformational changes. The 30S structure is color-coded as in panel B, but semi-transparent. Sgm is shown as a solid ribbon in blue; target G1405 is shown in yellow and helix 44 is shown in white.