332D

CRYSTAL STRUCTURE OF R(GUGUGUA)D(C) WITH TANDEM G-U/U-G WOBBLE PAIRS WITH STRAND SLIPPAGE

332D の概要

• エントリーDOI: 10.2210/pdb332d/pdb
• 分子名称: DNA/RNA (5'-R(*GP*UP*GP*UP*GP*UP*AP*)-D(*C)-3') (2 entities in total)
• 機能のキーワード: a-dna/rna, double helix, overhanging base, dna-rna complex, dna/rna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 5055.09

構造登録者

Biswas, R.,Sundaralingam, M. (登録日: 1997-05-14, 公開日: 1997-09-23, 最終更新日: 2024-04-03)

主引用文献

Biswas, R.,Sundaralingam, M.
Crystal structure of r(GUGUGUA)dC with tandem G x U/U x G wobble pairs with strand slippage.
J.Mol.Biol., 270:511-519, 1997

PubMed Abstract: To better understand the frequent occurrence of adjacent wobble pairs in ribosomal RNAs we have determined the crystal structure of the RNA duplex, r(GUGUGUA)dC with the 3'-terminal deoxy C residue. Two different crystal forms of the duplex were obtained and both belong to the rhombohedral space group, R3. Crystal form I has hexagonal unit cell dimensions, a = b = 40.82 A and c = 66.09 A and diffracts to 1.58 A resolution, while crystal form II has a = b = 47.11 A and c = 59.86 A, diffracting only to 2.50 A resolution. Both structures were solved by the molecular replacement method using different starting models. In spite of the large differences in the cell dimensions the overall structures in both crystals are similar. Instead of the expected blunt-end duplex with four consecutive G x U pairs, the slippage of the strands resulted in two different tandem G x U/U x G wobble pairs involving two of the central and two of the 5' overhang bases, still yielding a total of four wobble pairs. These tandem wobble pairs are flanked by two Watson-Crick pairs. The A-type duplexes stack in the familiar head-to-tail fashion forming a pseudocontinuous helix. The wobble pairs of the present motif II (G x U/U x G) structure stack with a low twist angle of 25.3 degrees in contrast to that of motif I (U x G/G x U), 38.1 degrees. The four wobble pairs are characteristically heavily hydrated in both the grooves accounting for their stability.

PubMed: 9237915
DOI: 10.1006/jmbi.1997.1118

実験手法

X-RAY DIFFRACTION (1.58 Å)