View source for 1kbd


==SOLUTION STRUCTURE OF A 16 BASE-PAIR DNA RELATED TO THE HIV-1 KAPPA B SITE==
<StructureSection load='1kbd' size='340' side='right'caption='[[1kbd]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kbd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KBD 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kbd OCA], [https://pdbe.org/1kbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kbd RCSB], [https://www.ebi.ac.uk/pdbsum/1kbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kbd ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex.,Tisne C, Hantz E, Hartmann B, Delepierre M J Mol Biol. 1998 May 29;279(1):127-42. PMID:9636705<ref>PMID:9636705</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Delepierre M]]
[[Category: Hantz E]]
[[Category: Hartmann B]]
[[Category: Tisne C]]