Introduction - This script shows a single-stranded RNA-binding protein, sex lethal from Drosophila melanogaster. Scroll down until the text corresponding to the view is visible. (based on 1b7f.pdb, H. Handa, et al., Nature 398, 579 (1999)).
The protein contains two RNA-binding domains which are composed of four antiparallel b-sheets connected by a-helices. RNA binds to one side of the sheet. and the a-helices occupy the other side of the sheet. Note how the RNA is bound in a highly bent conformation.
In this view all the residues in the RNA and the Protein that interact are shown in spacefill. Because the RNA is single-stranded, all the hydrogen bonding groups in the bases are available to interact with the protein. In addition, there are three hydrogen bonds formed between the 2'-OH of the ribose and the protein. These hydrogen bonds account for the fact that the protein has low affinity for DNA.