2KOC

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

Summary for 2KOC

• Entry DOI: 10.2210/pdb2koc/pdb
• NMR Information: BMRB: 5705
• Descriptor: RNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3') (1 entity in total)
• Functional Keywords: rna, uucg tetraloop, 14-mer hairpin
• Total number of polymer chains: 1
• Total formula weight: 4454.68

Authors

Nozinovic, S.,Fuertig, B.,Jonker, H.R.A.,Richter, C.,Schwalbe, H. (deposition date: 2009-09-17, release date: 2009-12-01, Last modification date: 2024-05-15)

Primary citation

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

Experimental method

SOLUTION NMR