2AO5

Crystal structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G-U base pairs

2AO5 の概要

• エントリーDOI: 10.2210/pdb2ao5/pdb
• 分子名称: 5'-R(*GP*GP*CP*GP*(5BU)P*GP*CP*GP*CP*U)-3', MAGNESIUM ION (3 entities in total)
• 機能のキーワード: g-u base pair, rna duplex, rna
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 13175.68

構造登録者

Utsunomiya, R.,Suto, K.,Balasundaresan, D.,Fukamizu, A.,Kumar, P.K.,Mizuno, H. (登録日: 2005-08-12, 公開日: 2006-03-28, 最終更新日: 2024-03-13)

主引用文献

Utsunomiya, R.,Suto, K.,Balasundaresan, D.,Fukamizu, A.,Kumar, P.K.,Mizuno, H.
Structure of an RNA duplex r(GGCGBrUGCGCU)2 with terminal and internal tandem G.U base pairs.
Acta Crystallogr.,Sect.D, 62:331-338, 2006

PubMed Abstract: The crystal structure of a self-complementary RNA duplex r(GGCG(Br)UGCGCU)(2) with terminal G.U and internal tandem G.U base pairs has been determined at 2.1 Angstroms resolution. The crystals belong to the tetragonal space group P4(3), with unit-cell parameters a = b = 37.69, c = 96.28 Angstroms and two duplexes in the asymmetric unit. The two strands of each duplex are related by a pseudodyad axis. The structure was refined to final R(work) and R(free) values of 20.9 and 25.3%, respectively. The duplexes stack in an end-to-end manner, forming infinite columns along the c axis. This is the first structural study of an RNA duplex containing G.U pairs at the termini. The stacking overlaps of the terminal G.U base pairs with their adjacent Watson-Crick base pairs are larger than those of Watson-Crick base pairs of the 5'-YR-3'/3'-RY-5' type. The terminal G.U base pairs of neighbouring duplexes are also stacked with each other. An alternating underwound-overwound pattern of the twist angles is seen at each step along the duplex. This observation is typical for internal tandem G.U pairs, while the terminal G.U base pairs exhibit high twist angles with the adjacent Watson-Crick pairs. The 3'-side of U of the internal G.U base pair, which is unstacked, appears to be stabilized by pi-cation interaction with an Mg(2+) ion.

PubMed: 16510980
DOI: 10.1107/S0907444905043210

実験手法

X-RAY DIFFRACTION (2.1 Å)