The small ribosomal subunit from Thermus thermophilus at 4.5 angstrom resolution: Pattern fittings and the identification of a functional site

The electron density map of the small ribosomal subunit from Thermus thermo philus, constructed at 4.5 Angstrom resolution, shows the recognizable morp hology of this particle, as well as structural features that were interpret ed as ribosomal RNA and proteins. Unbiased assignments, carried out by quan titative covalent binding of heavy atom compounds at predetermined sites, l ed to the localization of the surface of the ribosomal protein S13 at a pos ition compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the f old of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of th e initiation complex by a mercurated mRNA analog, led to the characterizati on of its vicinity.