Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface

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Abstract
The 7.8 angstrom crystal structure of the 70Sribosome reveals a discrete double-helical bridge (B4) that projects from the 50Ssubunit, making contact with the 30Ssubunit. Preliminary modeling studies localized its contact site, near the bottom of the platform, to the binding site for ribosomal protein S15. Directed hydroxyl radical probing from iron(II) tethered to S15 specifically cleaved nucleotides in the 715 loop of domain II of 23Sribosomal RNA, one of the known sites in 23Sribosomal RNA that are footprinted by the 30Ssubunit. Reconstitution studies show that protection of the 715 loop, but none of the other 30S-dependent protections, is correlated with the presence of S15 in the 30Ssubunit. The 715 loop is specifically protected by binding free S15 to 50Ssubunits. Moreover, the previously determined structure of a homologous stem-loop from U2 small nuclear RNA fits closely to the electron density of the bridge.