1IK5

Crystal Structure of a 14mer RNA Containing Double UU Bulges in Two Crystal Forms: A Novel U*(AU) Intramolecular Base Triple

1IK5 の概要

• エントリーDOI: 10.2210/pdb1ik5/pdb
• 分子名称: 5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3', 5'-R(*GP*GP*UP*AP*UP*UP*UP*UP*GP*GP*UP*AP*(CBR)P*C)-3', MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: rna duplex, uu-bulges, base triple, kink, rna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 9056.69

構造登録者

Deng, J.,Xiong, Y.,Sudarsanakumar, C.,Shi, K.,Sundaralingam, M. (登録日: 2001-05-02, 公開日: 2001-11-09, 最終更新日: 2024-02-07)

主引用文献

Deng, J.,Xiong, Y.,Sudarsanakumar, C.,Shi, K.,Sundaralingam, M.
Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple.
RNA, 7:1425-1431, 2001

PubMed Abstract: The RNA/DNA 14-mer, (gguauuucgguaCc)2 with consecutive uridine bulges (underlined) on each strand has been determined in two crystal forms, spermine bound (Sp-form) and spermine free (Sp-free). The former was solved by the MAD method with three-wavelength data collected at Brookhaven National Laboratory (BNL); the later isomorphous structure was solved by the molecular replacement method using data collected on our Raxis IIc imaging plate system. The two crystal forms belong to the space group C2 with one molecule of double-stranded 14 mer in the asymmetric unit. The Sp-form has cell constants, a = 60.06, b = 29.10, c = 52.57 A, beta = 120.79 degrees and was refined to 1.7 A resolution with a final Rwork/Rfree of 19.8%/22.7% using 8,549 independent reflections. The Sp-free structure has cell constants, a = 60.06, b = 29.58, c = 52.50 A, beta = 120.85 degrees and was refined to 1.8 A with a final Rwork/ Rfree of 20.8%/23.2% using 6,285 unique reflections. The two structures are identical, except that the Sp-form has a spermine bound in the major groove, parallel to the RNA helical axis. One of the uridine bulges forms a novel intramolecular U*(A x U) base triple. The helices are in the C3'-endo conformation (A-form), but the bulges adopt the C2'-endo sugar pucker. Furthermore, the bulges induce a kink (30 degrees) in the helix axis and a very large twist (55 degrees) between the base pairs flanking the bulges. The Sp-form has one Mg2+ ion whereas the Sp-free form has two Mg2+ ions.

PubMed: 11680847

実験手法

X-RAY DIFFRACTION (1.8 Å)