Structure of Xenopus Laevis 5S rRNA as Determined by Solution Data and Computer Graphic Modeling

A detailed atomic model of the eukaryotic oocyte 5S rRNA from Xenopus laevis has been built using computer modeling. The model integrates stereochemical constraints and experimental data on the accessibility of bases and phosphates towards several structure-specific probes. In spite of some uncertainty in the relative orientation of the substructures, several conclusions have been reached: (i) the model adopts a distorted Y-shaped structure; (ii) no long-range tertiary interaction occurs but the internal loops adopt particular conformation containing non-canonical base pairs. In this paper, the model is corroborated by the structural analysis of several mutants of loop c.