|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop== | | ==NMR solution structure of a 14-mer hairpin RNA with cUUCGg tetraloop== |
| - | <StructureSection load='2koc' size='340' side='right' caption='[[2koc]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2koc' size='340' side='right'caption='[[2koc]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2koc]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KOC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2koc]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KOC FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2koc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2koc OCA], [http://pdbe.org/2koc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2koc RCSB], [http://www.ebi.ac.uk/pdbsum/2koc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2koc ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2koc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2koc OCA], [https://pdbe.org/2koc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2koc RCSB], [https://www.ebi.ac.uk/pdbsum/2koc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2koc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 19: |
Line 20: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Fuertig, B]] | + | [[Category: Large Structures]] |
| - | [[Category: Jonker, H R.A]] | + | [[Category: Fuertig B]] |
| - | [[Category: Nozinovic, S]] | + | [[Category: Jonker HRA]] |
| - | [[Category: Richter, C]] | + | [[Category: Nozinovic S]] |
| - | [[Category: Schwalbe, H]] | + | [[Category: Richter C]] |
| - | [[Category: 14-mer hairpin]]
| + | [[Category: Schwalbe H]] |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Uucg tetraloop]]
| + | |
| Structural highlights
Publication Abstract from PubMed
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.
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.,Nozinovic S, Furtig B, Jonker HR, Richter C, Schwalbe H Nucleic Acids Res. 2010 Jan;38(2):683-94. Epub 2009 Nov 11. PMID:19906714[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nozinovic S, Furtig B, Jonker HR, Richter C, Schwalbe H. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res. 2010 Jan;38(2):683-94. Epub 2009 Nov 11. PMID:19906714 doi:10.1093/nar/gkp956
|
