The three-dimensional structure of yeast phenylalanine transfer RNA: shape of the molecule at 5.5-A resolution

Three isomorphous heavy-atom derivatives have been obtained of orthorhombic crystals of phenylalanine transfer RNA from yeast. These derivatives contain osmium, samarium, and platinum. The positions of the heavy atoms have been determined; these have been used to calculate a three-dimensional electron-density map of transfer RNA at a resolution of 5.5 A. The map shows a high contrast between the molecular boundaries and the solvent areas, so that most of the external shape of the molecule can be determined. The molecule appears to be 92 A long and to have a width varying from 16 A to 34 A. There are some narrow regions in the molecule that connect more globular regions. The electron density map shows chains of dense objects approximately 6 A apart that are probably due to adjacent phosphate groups on the polynucleotide chain. At the present stage of the analysis it is not possible to trace the entire backbone unambiguously; however, the data at this resolution suggest no apparent similarity between the folding of the molecule and any of the tertiary structure models proposed for transfer RNA.