2JWV

Structure of a high affinity anti-NFkB RNA aptamer

2JWV の概要

• エントリーDOI: 10.2210/pdb2jwv/pdb
• 関連するPDBエントリー: 1OOA
• NMR情報: BMRB: 15538
• 分子名称: RNA (29-MER) (1 entity in total)
• 機能のキーワード: rna, asymmetric internal bulge, stem loop
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 9326.56

構造登録者

Reiter, N.J.,Maher III, L.,Butcher, S.E. (登録日: 2007-10-25, 公開日: 2008-01-08, 最終更新日: 2024-05-01)

主引用文献

Reiter, N.J.,Maher, L.J.,Butcher, S.E.
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer
Nucleic Acids Res., 36:1227-1236, 2008

PubMed Abstract: The binding of RNA molecules to proteins or other ligands can require extensive RNA folding to create an induced fit. Understanding the generality of this principle involves comparing structures of RNA before and after complex formation. Here we report the NMR solution structure of a 29-nt RNA aptamer whose crystal structure had previously been determined in complex with its transcription factor target, the p50(2) form of NF-kappaB. The RNA aptamer internal loop structure has pre-organized features that are also found in the complex, including non-canonical base pairing and cross-strand base stacking. Remarkably, the free RNA aptamer structure possesses a major groove that more closely resembles B-form DNA than RNA. Upon protein binding, changes in RNA structure include the kinking of the internal loop and distortion of the terminal tetraloop. Thus, complex formation involves both pre-formed and induced fit binding interactions. The high affinity of the NF-kappaB transcription factor for this RNA aptamer may largely be due to the structural pre-organization of the RNA that results in its ability to mimic DNA.

PubMed: 18160411
DOI: 10.1093/nar/gkm1141

実験手法

SOLUTION NMR