1XWP

Solution structure of AUCGCA loop

1XWP の概要

• エントリーDOI: 10.2210/pdb1xwp/pdb
• 関連するPDBエントリー: 1XWU
• 分子名称: 5'-R(*GP*GP*AP*GP*AP*UP*CP*GP*CP*AP*CP*UP*CP*CP*A)-3' (1 entity in total)
• 機能のキーワード: hairpin loop, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 4790.93

構造登録者

Sakamoto, T.,Oguro, A.,Kawai, G.,Ohtsu, T.,Nakamura, Y. (登録日: 2004-11-02, 公開日: 2005-02-15, 最終更新日: 2024-05-29)

主引用文献

Sakamoto, T.,Oguro, A.,Kawai, G.,Ohtsu, T.,Nakamura, Y.
NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A
Nucleic Acids Res., 33:745-754, 2005

PubMed Abstract: A high affinity RNA aptamer (APT58, 58 nt long) against mammalian initiation factor 4A (eIF4A) requires nearly its entire nucleotide sequence for efficient binding. Since splitting either APT58 or eIF4A into two domains diminishes the affinity for each other, it is suggested that multiple interactions or a global interaction between the two molecules accounts for the high affinity. To understand the structural basis of APT58's global recognition of eIF4A, we determined the solution structure of two essential nucleotide loops (AUCGCA and ACAUAGA) within the aptamer using NMR spectroscopy. The AUCGCA loop is stabilized by a U-turn motif and contains a non-canonical A:A base pair (the single hydrogen bond mismatch: Hoogsteen/Sugar-edge). On the other hand, the ACAUAGA loop is stabilized by an AUA tri-nucleotide loop motif and contains the other type of A:A base pair (single hydrogen bond mismatch: Watson-Crick/Watson-Crick). Considering the known structural and functional properties of APT58, we propose that the AUCGCA loop is directly involved in the interaction with eIF4A, while the flexibility of the ACAUAGA loop is important to support this interaction. The Watson-Crick edges of C7 and C9 in the AUCGCA loop may directly interact with eIF4A.

PubMed: 15687383
DOI: 10.1093/nar/gki222

実験手法

SOLUTION NMR