A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit

AbstractThe 50S subunit of the ribosome catalyzes the peptidyl-transferase reaction of protein synthesis. We have generated X-ray crystallographic electron density maps of the large ribosomal subunit from Haloarcula marismortui at various resolutions up to 9 Å using data from crystals that diffract to 3 Å. Positioning a 20 Å resolution EM image of these particles in the crystal lattice produced phases accurate enough to locate the bound heavy atoms in three derivatives using difference Fourier maps, thus demonstrating the correctness of the EM model and its placement in the unit cell. At 20 Å resolution, the X-ray map is similar to the EM map; however, at 9 Å it reveals long, continuous, but branched features whose shape, diameter, and right-handed twist are consistent with segments of double-helical RNA that crisscross the subunit

Metals, Motifs, and Recognition in the Crystal Structure of a 5S rRNA Domain

AbstractTwo new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 Å, respectively. This loop E region is distorted by three “cross-strand purine stacks” and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface