A small-angle and wide-angle x-ray scattering study of the shape and secondary structure of native 5 S RNA from rat liver ribosomes.

Native 5 S RNA from rat liver ribosomes was investigated by means of small-angle and wide-angle X-ray scattering. The radius of gyration, Rs of the molecule is 3.1 nm, the maximum dimension, L, 10.5 nm and the shape volume, Vc, about 60 nm3. The overall shape of the molecule as derived from these parameters is a flat elliptical cylinder with dimensions of 2a = 10.45 nm, 2b = 6.94 nm, H = 1.06 nm. The cross-section radius of gyration of 0.92 nm and the mass per unit length of 2610 mol X nm-1 of the 5 S RNA molecule are typical for a double helical organized RNA molecule. From wide-angle scattering data it can be concluded that the double helical regions are in the A-form characterized by an 11-fold helix with a turn angle of 32.7 degrees and a distance of 0.28 nm between adjacent base pairs. A refined electron density model of a distorted L shape is proposed for the 5 S RNA molecule.