Comparison of the structures of the native form of rat liver 5S rRNA and yeast tRNA phe: small-angle and wide-angle X-ray scattering study

Abstract

The small-angle and wide-angle X-ray scattering of tRNA phe (yeast) and ribosomal 5S RNA (rat liver) in solution have been analysed and compared. tRNA phe in solution is folded into a compact L-shaped structure similar to its structure in crystals. The geometry of the secondary structure of the double helical regions is also equivalent to the A-form in the crystalline state. Despite differences between the molar mosses of 5S rRNA (40 000 g mol −1) and tRNA phe (25 000 g mol −1), and the fact that the 5S rRNA molecule is more anisometric than the tRNA phe molecule, there are many structural similarities. The geometrical parameters of the secondary structure of double helical regions in both RNA molecules are almost identical; the mean rise per base pair is about 0.253–0.28 nm and the mean turn angle is about 32.5–33.5. Identical cross-sectional radii of gyration, R sq,1 ≈ 1.16 nm and R sq,2 = 0.92 nm, identical molar mass per unit length, M Δx = 2500 g mol −1 nm −1 , and a mean thickness of the molecules D ≈ 1.65 nm suggest a similar, nearly coplanar organization of isolated, double helical arms. Furthermore, there are compact regions in the central parts of both molecules, which are the sites of tertiary interactions in the tRNA phe molecule and are a potential site of tertiary interactions in the SS rRNA molecule for stabilization of the complicated L-shape of the two molecules. Both molecules have a pseudo-twofold axis,w hich may play a role in recognition for binding of specific proteins.