View source for 2juk


==guanidino neomycin B recognition of an HIV-1 RNA helix==
<StructureSection load='2juk' size='340' side='right'caption='[[2juk]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2juk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JUK FirstGlance]. <br>
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G0B:(1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl+2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside'>G0B</scene></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=2juk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2juk OCA], [https://pdbe.org/2juk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2juk RCSB], [https://www.ebi.ac.uk/pdbsum/2juk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2juk ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.

Guanidinoneomycin B recognition of an HIV-1 RNA helix.,Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE Chembiochem. 2008 Jan 4;9(1):93-102. PMID:18058789<ref>PMID:18058789</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2juk" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Butcher SE]]
[[Category: Elson-Schwab L]]
[[Category: Niccolai N]]
[[Category: Staple DW]]
[[Category: Tor Y]]
[[Category: Venditti V]]