Crystallographic refinement of yeast phenylalanine transfer RNA at 2·5Å resolution

Abstract

We have refined the crystal structure of yeast tRNAPhe at 2·5Å resolution, using real-space refinement and improved electron density maps. The refinement has confirmed almost all the structural details found earlier by fitting a wire model to the map in an optical comparator. The hydrogen-bonding network running through the molecule is described in detail: 41 hydrogen bonds are listed, apart from the 54 in the base-pairs of the double-helical stems. Almost half involve 2′-OH groups of the riboses as acceptors, donors or both. A number of new conformational principles have emerged. We have found correlations between some of the nucleotide torsion angles and the pucker of the ribose ring, and have also found a small number of preferred ways in which a polynucleotide chain can bend or stretch. The pitch of the double helices in tRNA is rather less than in RNA fibres (although the other helical parameters are much the same). We believe this to be a consequence of the different environments of the two structures; in tRNA there is evidence for stabilizing interactions between 2′-OH of one ribose and Ol′ of its neighbour. The electron density maps give an indication of the degree of thermal motion and disorder in the molecule. The anticodon, the free end of the amino acid stem, and parts of the dhU† and extra loops show only weak density, whereas the TΨC and augmented dhU helices are rigid, and have well-defined density.