Identification of an RNA-protein bridge spanning the ribosomal subunit interface

The 7.8 angstrom crystal structure of the 70S ribosome reveals a discrete d ouble-helical bridge (B4) that projects from the 50S subunit, making contac t with the 30S subunit. Preliminary modeling studies Localized its contact site, near the bottom of the platform, to the binding site for ribosomal pr otein S15. Directed hydroxyl radical probing from iron(II) tethered to S15 specifically cleaved nucleotides in the 715 Loop of domain II of 23S riboso mal RNA, one of the known sites in 23S ribosomal RNA that are footprinted b y the 30S subunit. Reconstitution studies show that protection of the 715 L oop, but none of the other 30S-dependent protections, is correlated with th e presence of S15 in the 30S subunit. The 715 loop is specifically protecte d by binding free S15 to 50S subunits. Moreover, the previously determined structure of a homologous stem-loop from U2 small nuclear RNA fits closely to the electron density of the bridge.