2KOC

NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop

2KOC の概要

• エントリーDOI: 10.2210/pdb2koc/pdb
• NMR情報: BMRB: 5705
• 分子名称: RNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3') (1 entity in total)
• 機能のキーワード: rna, uucg tetraloop, 14-mer hairpin
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 4454.68

構造登録者

Nozinovic, S.,Fuertig, B.,Jonker, H.R.A.,Richter, C.,Schwalbe, H. (登録日: 2009-09-17, 公開日: 2009-12-01, 最終更新日: 2024-05-15)

主引用文献

Nozinovic, S.,Furtig, B.,Jonker, H.R.A.,Richter, C.,Schwalbe, H.
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA
Nucleic Acids Res., 2009

PubMed Abstract: We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 A) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.

PubMed: 19906714
DOI: 10.1093/nar/gkp956

実験手法

SOLUTION NMR