472D

STRUCTURE OF AN OCTAMER RNA WITH TANDEM GG/UU MISPAIRS

472D の概要

• エントリーDOI: 10.2210/pdb472d/pdb
• 分子名称: RNA (5'-R(*GP*UP*GP*UP*UP*UP*AP*C)-3'), RNA (5'-R(*GP*UP*AP*GP*GP*CP*AP*C)-3') (3 entities in total)
• 機能のキーワード: gg/uu mispairs, ribonucleic acid, rna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 5070.11

構造登録者

Deng, J.,Sundaralingam, M. (登録日: 1999-05-14, 公開日: 2000-11-27, 最終更新日: 2023-12-27)

主引用文献

Deng, J.,Sundaralingam, M.
Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs.
Nucleic Acids Res., 28:4376-4381, 2000

PubMed Abstract: We have determined the crystal structure of the RNA octamer duplex r(guguuuac)/r(guaggcac) with a tandem wobble pair, G.G/U.U (motif III), to compare it with U.G/G.U (motif I) and G.U/U.G (motif II) and to better understand their relative stabilities. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 41.92 A, c = 56.41 A, and gamma = 120 degrees, with one duplex in the asymmetric unit. The structure was solved by the molecular replacement method at 1.9 A resolution and refined to a final R: factor of 19.9% and R(free) of 23.3% for 2862 reflections in the resolution range 10.0-1.9 A with F >/= 2sigma(F). The final model contains 335 atoms for the RNA duplex and 30 water molecules. The A-RNA stacks in the familiar head-to-tail fashion forming a pseudo-continuous helix. The uridine bases of the tandem U.G pairs have slipped towards the minor groove relative to the guanine bases and the uridine O2 atoms form bifurcated hydrogen bonds with the N1 and N2 of guanines. The N2 of guanine and O2 of uridine do not bridge the 'locked' water molecule in the minor groove, as in motifs I and II, but are bridged by water molecules in the major groove. A comparison of base stacking stabilities of motif III with motifs I and II confirms the result of thermodynamic studies, motif I > motif III > motif II.

PubMed: 11058138
DOI: 10.1093/nar/28.21.4376

実験手法

X-RAY DIFFRACTION (1.9 Å)