Small-angle x-ray scattering study of S4-RNA, the 16 S RNA binding site for the protein S4 from Escherichia coli ribosomes

Abstract

The ribonucleic acid (16 S RNA) of the 30 S Escherichia coli ribosomal subunit binds many of the proteins in this subunit, such as, for instance, S4, S7, S8, S15 and S20 [1,2]. The 16 S RNA binding site for the S4 protein, S4-RNA, can be isolated in pure form [3-91 ; and it is indicated that this binding site consists mainly of two regions of approximately 150 and 160 nucleotides, originating from the 5’ terminal third of the 16 S RNA molecule [7]. These two regions, which are separated by about 120 nucleotides of the 16 S RNA sequence, seem to be stabilized by a specific RNA-RNA interaction [7] . Although the sequence of the S4-RNA region, prepared with both T1 and pancreatic ribonucleases, has been partially analysed [7,9], the correct molecular weight and the size and shape of S4-RNA are not known. We have analysed S4-RNA by using the small-angle X-ray scattering method; the results yield a molecular weight of 136 000 and a radius of gyration of 43.5 A. The X-ray scattering curve can be explained, in its proximal angular range, by the scattering from a twoparameter, uniform electron density model with a shape of an oblate ellipsoid and the dimensions of 132 X 132 X 32 a. 2. Materials and methods