Placement of protein and RNA structures into a 5 angstrom-resolution map of the 50S ribosomal subunit

We have calculated at 5.0 Angstrom resolution an electron-density map of th e large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A -form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate doubl e helices, not all of which are A-form, and in many places proteins crossli nk two or more of these rods. The polypeptide exit channel was marked by tu ngsten cluster compounds bound in one heavy-atom-derivatized crystal. We ha ve determined the structure of the translation-factor-binding centre by fit ting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin-ricin loop RNA, and the RNA sequence that binds L11 into the electro n density. We can position either elongation factor a or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-bin ding centre in a manner that is consistent with results from biochemical an d electron microscopy studies.