Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge

The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 Angstrom (Form I, space group P4(2)2(1)2, a = b - 57.15 Angstrom and c = 43.54 Angstrom) and 1.7 Angstrom (Form II, space group P4(3)2(1)2, a = b = 32.78 Angstrom and c = 102.5 Angstrom), The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 Angstrom. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 Angstrom. In Form I, the cytosine bulge forms an intermolecular (C) under bar(+)*G.C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4 (C) under bar and O6G, and between protonated N3(+)(C) under bar and N7G. In contrast, a minor groove (C) under bar*G.C triple is formed in Form II with intermolecular hydrogen bonds between O2 (C) under bar and N2G, and between N3 (C) under bar and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.