3rkq - Revision history

OCA at 09:43, 1 March 2024

OCA — Fri, 01 Mar 2024 09:43:30 GMT

←Older revision		Revision as of 09:43, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3rkq' size='340' side='right'caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3rkq' size='340' side='right'caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rkq]] is a 4 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=3RKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NKX2-5, CSX, NKX2.5, NKX2E ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [https://pdbe.org/3rkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [https://www.ebi.ac.uk/pdbsum/3rkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkq 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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [https://pdbe.org/3rkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [https://www.ebi.ac.uk/pdbsum/3rkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkq ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4 (By similarity). It is transcriptionally controlled by PBX1 and acts as a transcriptional repressor of CDKN2B (By similarity). It is required for spleen development.<ref>PMID:22560297</ref>	+	[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN] Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4 (By similarity). It is transcriptionally controlled by PBX1 and acts as a transcriptional repressor of CDKN2B (By similarity). It is required for spleen development.<ref>PMID:22560297</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 A resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.	+

-	~~Crystal structure of the human~~ NKX2.5 ~~homeodomain in complex with DNA target~~.~~,Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ Biochemistry. 2012 Aug 14;51(32):6312-9. Epub 2012 Aug 3. PMID:22849347<ref>PMID:22849347</ref>~~	+	==See Also==
-		+	*[[NKX2.5 Homeodomain\|NKX2.5 Homeodomain]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rkq" style="background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Genis, C]]	+	[[Category: Genis C]]
-	[[Category: Kasahara, H]]	+	[[Category: Kasahara H]]
-	[[Category: Nam, H J]]	+	[[Category: Nam H-J]]
-	[[Category: Scone, P]]	+	[[Category: Scone P]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 10:14, 22 June 2022

OCA — Wed, 22 Jun 2022 10:14:53 GMT

←Older revision		Revision as of 10:14, 22 June 2022
Line 1:		Line 1:

	==NKX2.5 Homeodomain dimer bound to ANF-242 DNA==		==NKX2.5 Homeodomain dimer bound to ANF-242 DNA==
-	<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='3rkq' size='340' side='right'caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [~~http~~://pdbe.org/3rkq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rkq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkq 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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [https://pdbe.org/3rkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [https://www.ebi.ac.uk/pdbsum/3rkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkq ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4 (By similarity). It is transcriptionally controlled by PBX1 and acts as a transcriptional repressor of CDKN2B (By similarity). It is required for spleen development.<ref>PMID:22560297</ref>	+	[[https://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4 (By similarity). It is transcriptionally controlled by PBX1 and acts as a transcriptional repressor of CDKN2B (By similarity). It is required for spleen development.<ref>PMID:22560297</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Genis, C]]		[[Category: Genis, C]]
	[[Category: Kasahara, H]]		[[Category: Kasahara, H]]

OCA at 11:44, 11 August 2016

OCA — Thu, 11 Aug 2016 11:44:41 GMT

←Older revision		Revision as of 11:44, 11 August 2016
Line 1:		Line 1:
		+
	==NKX2.5 Homeodomain dimer bound to ANF-242 DNA==		==NKX2.5 Homeodomain dimer bound to ANF-242 DNA==
	<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [http://www.ebi.ac.uk/pdbsum/3rkq 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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [http://pdbe.org/3rkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [http://www.ebi.ac.uk/pdbsum/3rkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rkq ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 19:		Line 20:
	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 3rkq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:31, 4 January 2015

OCA — Sun, 04 Jan 2015 10:31:20 GMT

←Older revision		Revision as of 10:31, 4 January 2015
Line 2:		Line 2:
	<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. <br>	+	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RKQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [http://www.ebi.ac.uk/pdbsum/3rkq PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [http://www.ebi.ac.uk/pdbsum/3rkq PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.		[[http://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
Line 18:		Line 17:
	Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.,Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ Biochemistry. 2012 Aug 14;51(32):6312-9. Epub 2012 Aug 3. PMID:22849347<ref>PMID:22849347</ref>		Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.,Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ Biochemistry. 2012 Aug 14;51(32):6312-9. Epub 2012 Aug 3. PMID:22849347<ref>PMID:22849347</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 25:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Genis, C.]]	+	[[Category: Genis, C]]
-	[[Category: Kasahara, H.]]	+	[[Category: Kasahara, H]]
-	[[Category: Nam, H J.]]	+	[[Category: Nam, H J]]
-	[[Category: Scone, P.]]	+	[[Category: Scone, P]]
	[[Category: Dna binding]]		[[Category: Dna binding]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 06:47, 14 May 2014

OCA — Wed, 14 May 2014 06:47:43 GMT

←Older revision		Revision as of 06:47, 14 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3rkq.~~jpg~~\|~~left~~\|~~200px~~]]	+	==NKX2.5 Homeodomain dimer bound to ANF-242 DNA==
		+	<StructureSection load='3rkq' size='340' side='right' caption='[[3rkq]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rkq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NKX2-5, CSX, NKX2.5, NKX2E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rkq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rkq RCSB], [http://www.ebi.ac.uk/pdbsum/3rkq PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Athyreosis;Familial isolated congenital asplenia;Atrial septal defect - atrioventricular conduction defects;Atrial septal defect, ostium secundum type;Hypoplastic left heart syndrome;Tetralogy of Fallot;Familial atrial fibrillation;Familial progressive cardiac conduction defect;Thyroid hypoplasia;Ventricular septal defect. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NKX25_HUMAN NKX25_HUMAN]] Implicated in commitment to and/or differentiation of the myocardial lineage. Acts as a transcriptional activator of ANF in cooperation with GATA4 (By similarity). It is transcriptionally controlled by PBX1 and acts as a transcriptional repressor of CDKN2B (By similarity). It is required for spleen development.<ref>PMID:22560297</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 A resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

-	~~<!--~~	+	Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.,Pradhan L, Genis C, Scone P, Weinberg EO, Kasahara H, Nam HJ Biochemistry. 2012 Aug 14;51(32):6312-9. Epub 2012 Aug 3. PMID:22849347<ref>PMID:22849347</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3rkq"~~, ~~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_3rkq\| PDB=3rkq \| SCENE= }}~~	+

-	~~===NKX2~~.~~5 Homeodomain dimer bound to ANF-242 DNA===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	==~~About this Structure~~==	+	<references/>
-	~~[[3rkq]] is a 4 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA].~~	+	__TOC__
-	[[Category: ~~Homo sapiens~~]]	+	</StructureSection>
		+	[[Category: Human]]
	[[Category: Genis, C.]]		[[Category: Genis, C.]]
	[[Category: Kasahara, H.]]		[[Category: Kasahara, H.]]

OCA at 09:19, 9 May 2012

OCA — Wed, 09 May 2012 09:19:07 GMT

←Older revision		Revision as of 09:19, 9 May 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3rkq.jpg\|left\|200px]]

-	The ~~entry 3rkq~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rkq", 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_3rkq\| PDB=3rkq \| SCENE= }}

-	~~Authors: Genis, C., Scone, P., Kasahara, H., Nam, H~~.-J.	+	===NKX2.5 Homeodomain dimer bound to ANF-242 DNA===

-	~~Description~~: ~~NKX2~~.~~5 Homeodomain dimer bound to ANF~~-~~242 DNA~~	+
		+	==About this Structure==
		+	[[3rkq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RKQ OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Genis, C.]]
		+	[[Category: Kasahara, H.]]
		+	[[Category: Nam, H J.]]
		+	[[Category: Scone, P.]]
		+	[[Category: Dna binding]]
		+	[[Category: Helix-turn-helix]]
		+	[[Category: Nucleus]]
		+	[[Category: Transcription-dna complex]]

OCA at 04:20, 12 May 2011

OCA — Thu, 12 May 2011 04:20:28 GMT

←Older revision		Revision as of 04:20, 12 May 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rkq is ON HOLD	+	The entry 3rkq is ON HOLD until Paper Publication

	Authors: Genis, C., Scone, P., Kasahara, H., Nam, H.-J.		Authors: Genis, C., Scone, P., Kasahara, H., Nam, H.-J.

	Description: NKX2.5 Homeodomain dimer bound to ANF-242 DNA		Description: NKX2.5 Homeodomain dimer bound to ANF-242 DNA

OCA: Protected "3rkq" [edit=sysop:move=sysop]

OCA — Wed, 27 Apr 2011 06:58:04 GMT

Protected "3rkq" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:58, 27 April 2011

OCA: New page: '''Unreleased structure''' The entry 3rkq is ON HOLD Authors: Genis, C., Scone, P., Kasahara, H., Nam, H.-J. Description: NKX2.5 Homeodomain dimer bound to ANF-242 DNA

OCA — Wed, 27 Apr 2011 06:58:03 GMT

New page: '''Unreleased structure''' The entry 3rkq is ON HOLD Authors: Genis, C., Scone, P., Kasahara, H., Nam, H.-J. Description: NKX2.5 Homeodomain dimer bound to ANF-242 DNA

New page

'''Unreleased structure'''

The entry 3rkq is ON HOLD

Authors: Genis, C., Scone, P., Kasahara, H., Nam, H.-J.

Description: NKX2.5 Homeodomain dimer bound to ANF-242 DNA