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| - | [[Image:2jwv.jpg|left|200px]] | |
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| - | <!--
| + | ==Structure of a high affinity anti-NFkB RNA aptamer== |
| - | The line below this paragraph, containing "STRUCTURE_2jwv", creates the "Structure Box" on the page.
| + | <StructureSection load='2jwv' size='340' side='right'caption='[[2jwv]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2jwv]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JWV FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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=2jwv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jwv OCA], [https://pdbe.org/2jwv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jwv RCSB], [https://www.ebi.ac.uk/pdbsum/2jwv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jwv ProSAT]</span></td></tr> |
| - | {{STRUCTURE_2jwv| PDB=2jwv | SCENE= }}
| + | </table> |
| - | | + | __TOC__ |
| - | '''Structure of a high affinity anti-NFkB RNA aptamer'''
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | | + | [[Category: Butcher SE]] |
| - | ==Overview== | + | [[Category: Maher III L]] |
| - | 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.
| + | [[Category: Reiter NJ]] |
| - | | + | |
| - | ==About this Structure== | + | |
| - | 2JWV is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JWV OCA].
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| - | ==Reference== | + | |
| - | DNA mimicry by a high-affinity anti-NF-{kappa}B RNA aptamer., Reiter NJ, Maher LJ 3rd, Butcher SE, Nucleic Acids Res. 2007 Dec 26;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18160411 18160411]
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| - | [[Category: Single protein]] | + | |
| - | [[Category: Butcher, S E.]] | + | |
| - | [[Category: III, L Maher.]] | + | |
| - | [[Category: Reiter, N J.]] | + | |
| - | [[Category: Asymmetric internal bulge]] | + | |
| - | [[Category: Rna]] | + | |
| - | [[Category: Stem loop]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 09:21:52 2008''
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