2kbd: Difference between revisions

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[[Image:2kbd.gif|left|200px]]
{{Seed}}
[[Image:2kbd.png|left|200px]]


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{{STRUCTURE_2kbd|  PDB=2kbd  |  SCENE=  }}  
{{STRUCTURE_2kbd|  PDB=2kbd  |  SCENE=  }}  


'''5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3''''
===5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'===




==Overview==
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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.
The line below this paragraph, {{ABSTRACT_PUBMED_9636705}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 9636705 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9636705}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KBD OCA].  


==Reference==
==Reference==
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[[Category: Modelling]]
[[Category: Modelling]]
[[Category: Nmr]]
[[Category: Nmr]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:28:52 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 07:49:49 2008''

Revision as of 04:49, 28 July 2008

File:2kbd.png

Template:STRUCTURE 2kbd

5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'

Template:ABSTRACT PUBMED 9636705

About this Structure

Full experimental information is available from OCA.

Reference

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

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