Crystal structures of two plasmid copy control related RNA duplexes: An 18base pair duplex at 1.20 A resolution and a 19 base pair duplex at 1.55 A resolution

The structures of two RNA duplexes, whose sequences correspond to portions of the ColE1 plasmid copy control RNA I and RNA II, have been determined. C rystals containing the 18mers 5'-CA CCGUUGGUAGCGGUGC-3' and 5'-CACCGCUACCAA CGGUGC-3' diffract to 1.20 Angstrom resolution while those containing the 1 9mers 5'-GCACCGUUGGUAGCGGUGC-3' and 5'-GCACCGCUACCAACGGUGC-3' diffract to 1 .55 Angstrom resolution. Both duplexes are standard A form, with Watson-Cri ck base pairing throughout. Use of anisotropic atomic displacement factors in refinement of the 1.20 Angstrom, structure dramatically improved refinem ent statistics, resulting in a final R-free of 15.0% and a crystallographic R-factor of 11.6%, Perhaps surprisingly, these crystals of the 18 base pai r RNA exhibit a 36-fold static disorder, resulting in a structure with a si ngle sugar-phosphate backbone conformation and an averaged base composition at each residue. Since the sugar-phosphate backbone structure is identical in the 36 different nucleotides that are superimposed, there can be no seq uence-dependent variation in the structure. The average ribose pucker ampli tude is 45.8 degrees for the 18 base pair structure and 46.4 degrees for th e 19 base pair structure; these values are respectively 19% and 20% larger than the average pucker amplitude reported from nucleoside crystal structur es. A standard RNA water structure, based on analysis of the hydration of t hese crystal structures and that of the TAR RNA stem [Ippolito, J. A., and Steitz, T. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9819-9824], has been derived, which has allowed us to predict water positions in lower resoluti on RNA crystal structures. We report a new RNA packing motif, in which thre e pro-S-p phosphate oxygens interact with an ammonium ion.