1sgs - Revision history

OCA at 21:35, 28 June 2023

OCA — Wed, 28 Jun 2023 21:35:57 GMT

←Older revision		Revision as of 21:35, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='1sgs' size='340' side='right'caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1sgs' size='340' side='right'caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [https://pdbe.org/1sgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [https://www.ebi.ac.uk/pdbsum/1sgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sgs ProSAT]</span></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [https://pdbe.org/1sgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [https://www.ebi.ac.uk/pdbsum/1sgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sgs ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fusco~~, A J~~]]	+	[[Category: Fusco AJ]]
-	[[Category: Ghosh, G]]	+	[[Category: Ghosh G]]
-	[[Category: Huang~~, D B~~]]	+	[[Category: Huang DB]]
-	[[Category: Phelps~~, C B]]~~	+	[[Category: Phelps CB]]
-	~~[[Category: Calcium binding]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Free kb dna]]~~	+
-	~~[[Category: Nf-kb binding~~]]	+

OCA at 07:31, 22 September 2021

OCA — Wed, 22 Sep 2021 07:31:11 GMT

←Older revision		Revision as of 07:31, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1sgs' size='340' side='right'caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1sgs' size='340' side='right'caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SGS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [~~http~~://pdbe.org/1sgs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sgs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sgs ProSAT]</span></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [https://pdbe.org/1sgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [https://www.ebi.ac.uk/pdbsum/1sgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sgs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:46, 11 December 2019

OCA — Wed, 11 Dec 2019 19:46:30 GMT

←Older revision		Revision as of 19:46, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of a free kB DNA==		==Crystal structure of a free kB DNA==
-	<StructureSection load='1sgs' size='340' side='right' caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1sgs' size='340' side='right'caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Fusco, A J]]		[[Category: Fusco, A J]]
	[[Category: Ghosh, G]]		[[Category: Ghosh, G]]

OCA at 07:16, 8 March 2018

OCA — Thu, 08 Mar 2018 07:16:59 GMT

←Older revision		Revision as of 07:16, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of a free kB DNA==		==Crystal structure of a free kB DNA==
	<StructureSection load='1sgs' size='340' side='right' caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1sgs' size='340' side='right' caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [http://pdbe.org/1sgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [http://www.ebi.ac.uk/pdbsum/1sgs PDBsum]</span></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [http://pdbe.org/1sgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [http://www.ebi.ac.uk/pdbsum/1sgs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sgs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:41, 11 September 2015

OCA — Fri, 11 Sep 2015 00:41:44 GMT

←Older revision		Revision as of 00:41, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [http://www.ebi.ac.uk/pdbsum/1sgs PDBsum]</span></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [http://pdbe.org/1sgs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [http://www.ebi.ac.uk/pdbsum/1sgs PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1sgs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:19, 3 January 2015

OCA — Sat, 03 Jan 2015 22:19:35 GMT

←Older revision		Revision as of 22:19, 3 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_1sgs\| PDB~~=1sgs \| ~~SCENE~~= }}	+	==Crystal structure of a free kB DNA==
-	===~~Crystal~~ structure of a ~~free kB DNA~~===	+	<StructureSection load='1sgs' size='340' side='right' caption='[[1sgs]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15663934}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SGS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1sgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sgs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sgs RCSB], [http://www.ebi.ac.uk/pdbsum/1sgs PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The dimeric NF-kappaB transcription factors regulate gene expression by recognizing specific DNA sequences located within the promoters of target genes. The DNA sequences, referred to as kappaB DNA, are divided into two broad classes. Class I kappaB DNA binds optimally to p50 and p52 NF-kappaB subunits, while class II kappaB DNAs are recognized specifically by the NF-kappaB subunits c-Rel and p65. We determined the X-ray crystal structure of a class II kappaB DNA sequence at 1.60 A resolution. This structure provides a detailed picture of kappaB DNA hydration, counter ion binding, and conformation in the absence of NF-kappaB binding partner. X-ray structures of both class I and class II kappaB DNA bound to NF-kappaB dimers were determined previously. Additionally, the NMR solution structure of a class I kappaB DNA is known. Comparison of the protein-bound and unbound kappaB DNA structures reveals that the free form of both classes approximates ideal B-form DNA more closely. Local geometries about specific DNA bases differ significantly upon binding to NF-kappaB. This is particularly evident at the 5'-GG/CC base-pairs; a signature of NF-kappaB specific DNA binding sequences. Differential phosphate group conformations, minor groove widths, buckle, twist, and tilt angles are observed between bound and unbound kappaB DNA. We observe that the presence of an extra G:C base-pair, 5'- to the GGA sequence in class I kappaB DNA, alters the geometry of the two internal G:C base-pairs within the GGGA tetranucleotide, which explains, at least in part, the structural basis for distinct NF-kappaB dimer recruitment by the two different classes of kappaB DNA. Together, these observations suggest that NF-kappaB dimers recognize specific structural features of kappaB DNA in order to make sequence-specific complexes.

-	~~==About this Structure==~~	+	Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB.,Huang DB, Phelps CB, Fusco AJ, Ghosh G J Mol Biol. 2005 Feb 11;346(1):147-60. Epub 2004 Dec 13. PMID:15663934<ref>PMID:15663934</ref>
-	~~[[1sgs]] is a 1 chain~~ structure~~. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il/oca~~-~~bin/ocashort?id=1SGS OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:015663934</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Fusco, A J.]]	+	== References ==
-	[[Category: Ghosh, G.]]	+	<references/>
-	[[Category: Huang, D B.]]	+	__TOC__
-	[[Category: Phelps, C B.]]	+	</StructureSection>
		+	[[Category: Fusco, A J]]
		+	[[Category: Ghosh, G]]
		+	[[Category: Huang, D B]]
		+	[[Category: Phelps, C B]]
	[[Category: Calcium binding]]		[[Category: Calcium binding]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Free kb dna]]		[[Category: Free kb dna]]
	[[Category: Nf-kb binding]]		[[Category: Nf-kb binding]]

OCA at 08:48, 23 April 2014

OCA — Wed, 23 Apr 2014 08:48:50 GMT

←Older revision		Revision as of 08:48, 23 April 2014
Line 1:		Line 1:
-	[[Image:1sgs.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1sgs", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1sgs\| PDB=1sgs \| SCENE= }}		{{STRUCTURE_1sgs\| PDB=1sgs \| SCENE= }}
-
	===Crystal structure of a free kB DNA===		===Crystal structure of a free kB DNA===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15663934}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15663934 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15663934}}		{{ABSTRACT_PUBMED_15663934}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:015663934</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015663934</ref><references group="xtra"/><references/>
	[[Category: Fusco, A J.]]		[[Category: Fusco, A J.]]
	[[Category: Ghosh, G.]]		[[Category: Ghosh, G.]]

OCA: Protected "1sgs" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 11:29:08 GMT

Protected "1sgs" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:29, 16 November 2011

OCA at 11:29, 16 November 2011

OCA — Wed, 16 Nov 2011 11:29:07 GMT

←Older revision		Revision as of 11:29, 16 November 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1sgs.png\|left\|200px]]		[[Image:1sgs.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA].	+	[[1sgs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SGS OCA].

	==Reference==		==Reference==
-	Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB., Huang DB, Phelps CB, Fusco AJ, Ghosh G, J Mol Biol. 2005 Feb 11;346(1):147-60. Epub 2004 Dec 13. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15663934 15663934]~~	+	<ref group="xtra">PMID:015663934</ref><references group="xtra"/>
	[[Category: Fusco, A J.]]		[[Category: Fusco, A J.]]
	[[Category: Ghosh, G.]]		[[Category: Ghosh, G.]]
Line 29:		Line 28:
	[[Category: Phelps, C B.]]		[[Category: Phelps, C B.]]
	[[Category: Calcium binding]]		[[Category: Calcium binding]]
		+	[[Category: Dna]]
	[[Category: Free kb dna]]		[[Category: Free kb dna]]
	[[Category: Nf-kb binding]]		[[Category: Nf-kb binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:48:32 2008''

OCA at 12:48, 28 July 2008

OCA — Mon, 28 Jul 2008 12:48:34 GMT

←Older revision		Revision as of 12:48, 28 July 2008
Line 1:		Line 1:
-	[[Image:1sgs.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1sgs.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1sgs\| PDB=1sgs \| SCENE= }}		{{STRUCTURE_1sgs\| PDB=1sgs \| SCENE= }}

-	~~'''~~Crystal structure of a free kB DNA~~'''~~	+	===Crystal structure of a free kB DNA===


-	~~==Overview==~~	+	<!--
-	The ~~dimeric NF-kappaB transcription factors regulate gene expression by recognizing specific DNA sequences located within the promoters of target genes. The DNA sequences~~, ~~referred to as kappaB DNA, are divided into two broad classes. Class I kappaB DNA binds optimally to p50 and p52 NF-kappaB subunits~~, ~~while class II kappaB DNAs are recognized specifically by~~ the NF-kappaB subunits c-Rel and p65. We determined the X-ray crystal structure of a class II kappaB DNA sequence at 1.60 A resolution. This structure provides a detailed picture of kappaB DNA hydration, counter ion binding, and conformation in the absence of NF-kappaB binding partner. X-ray structures of both class I and class II kappaB DNA bound to ~~NF-kappaB dimers were determined previously. Additionally,~~ the NMR solution structure of a class I kappaB DNA is known. Comparison of the protein-bound and unbound kappaB DNA structures reveals that the free form of both classes approximates ideal B-form DNA more closely. Local geometries about specific DNA bases differ significantly upon binding to NF-kappaB. This is particularly evident at ~~the 5'-GG~~/~~CC base-pairs; a signature of NF-kappaB specific DNA binding sequences~~. ~~Differential phosphate group conformations, minor groove widths, buckle, twist, and tilt angles are observed between bound and unbound kappaB DNA~~. ~~We observe that the presence of an extra G:C base-pair~~, ~~5'- to~~ the GGA sequence in class I kappaB DNA, alters the geometry of the two internal G:C base-pairs within the GGGA tetranucleotide, which explains, at least in part, the structural basis for distinct NF-kappaB dimer recruitment by the two different classes of kappaB DNA. ~~Together, these observations suggest that NF~~-~~kappaB dimers recognize specific structural features of kappaB DNA in order to make sequence~~-~~specific complexes.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_15663934}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15663934 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15663934}}

	==About this Structure==		==About this Structure==
Line 27:		Line 31:
	[[Category: Free kb dna]]		[[Category: Free kb dna]]
	[[Category: Nf-kb binding]]		[[Category: Nf-kb binding]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 08~~:41:03 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:48:32 2008''