4g1z - Revision history

OCA at 11:25, 1 March 2024

OCA — Fri, 01 Mar 2024 11:25:04 GMT

←Older revision		Revision as of 11:25, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [https://pdbe.org/4g1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [https://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z 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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [https://pdbe.org/4g1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [https://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref>		[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Actual use of the active form of vitamin D (calcitriol or 1alpha,25-dihydroxyvitamin D(3)) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. Structurally distinct nonsecosteroidal analogues have been developed to mimic calcitriol activity profiles with low calcium serum levels. Here, we report the crystallographic study of vitamin D nuclear receptor (VDR) ligand binding domain in complexes with six nonsecosteroidal analogues harboring two or three phenyl rings. These compounds induce a stimulated transcription in the nanomolar range, similar to calcitriol. Examination of the protein-ligand interactions reveals the mode of binding of these nonsecosteroidal compounds and highlights the role of the various chemical modifications of the ligands to VDR binding and activity, notably (de)solvation effects. The structures with the tris-aromatic ligands exhibit a rearrangement of a novel region of the VDR ligand binding pocket, helix H6.
-
-	Structural Basis for the Accommodation of Bis- and Tris-Aromatic Derivatives in Vitamin D Nuclear Receptor.,Ciesielski F, Sato Y, Chebaro Y, Moras D, Dejaegere A, Rochel N J Med Chem. 2012 Sep 19. PMID:22957834<ref>PMID:22957834</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4g1z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:40, 14 December 2022

OCA — Wed, 14 Dec 2022 10:40:59 GMT

←Older revision		Revision as of 10:40, 14 December 2022
Line 3:		Line 3:
	<StructureSection load='4g1z' size='340' side='right'caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4g1z' size='340' side='right'caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [https://pdbe.org/4g1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [https://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z 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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [https://pdbe.org/4g1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [https://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref> [[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>	+	[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Histone acetyltransferase~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ciesielski, F]]	+	[[Category: Ciesielski F]]
-	[[Category: Moras, D]]	+	[[Category: Moras D]]
-	[[Category: Rochel, N]]	+	[[Category: Rochel N]]
-	[[Category: Sato, Y]]	+	[[Category: Sato Y]]
-	~~[[Category: Alpha helical sandwich]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Nuclear receptor]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription-transcription inhibitor complex]]~~	+
-	~~[[Category: Vdr~~]]	+

OCA at 17:28, 10 March 2021

OCA — Wed, 10 Mar 2021 17:28:14 GMT

←Older revision		Revision as of 17:28, 10 March 2021
Line 1:		Line 1:

	==Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor==		==Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor==
-	<StructureSection load='4g1z' size='340' side='right' caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4g1z' size='340' side='right'caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [~~http~~://pdbe.org/4g1z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z 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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [https://pdbe.org/4g1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [https://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.	+	[[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref> [[~~http~~://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>	+	[[https://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref> [[https://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 29:
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Ciesielski, F]]		[[Category: Ciesielski, F]]
	[[Category: Moras, D]]		[[Category: Moras, D]]

OCA at 07:33, 4 August 2016

OCA — Thu, 04 Aug 2016 07:33:11 GMT

←Older revision		Revision as of 07:33, 4 August 2016
Line 1:		Line 1:
		+
	==Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor==		==Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor==
	<StructureSection load='4g1z' size='340' side='right' caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4g1z' size='340' side='right' caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Danio_rerio Danio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 ~~Danio~~ rerio])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [http://www.ebi.ac.uk/pdbsum/4g1z 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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [http://pdbe.org/4g1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [http://www.ebi.ac.uk/pdbsum/4g1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4g1z ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	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 4g1z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Danio~~ rerio]]	+	[[Category: Brachidanio rerio]]
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
	[[Category: Ciesielski, F]]		[[Category: Ciesielski, F]]

OCA at 10:59, 21 December 2014

OCA — Sun, 21 Dec 2014 10:59:47 GMT

←Older revision		Revision as of 10:59, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}~~	+	==Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor==
-	===Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor===	+	<StructureSection load='4g1z' size='340' side='right' caption='[[4g1z]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	{~~{ABSTRACT_PUBMED_22957834}~~}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4G1Z FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0VP:3-(5-{[3,4-BIS(HYDROXYMETHYL)BENZYL]OXY}-2-ETHYL-2-PROPYLBIPHENYL-4-YL)PENTAN-3-OL'>0VP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4g1d\|4g1d]], [[4g1y\|4g1y]], [[4g20\|4g20]], [[4g21\|4g21]], [[4g2h\|4g2h]], [[4g2i\|4g2i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vdra, nr1i1a, vdr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Danio rerio])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=4g1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4g1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4g1z RCSB], [http://www.ebi.ac.uk/pdbsum/4g1z PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.		[[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref> [[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Actual use of the active form of vitamin D (calcitriol or 1alpha,25-dihydroxyvitamin D(3)) to treat hyperproliferative disorders is hampered by calcemic effects, hence the continuous development of chemically modified analogues with dissociated profiles. Structurally distinct nonsecosteroidal analogues have been developed to mimic calcitriol activity profiles with low calcium serum levels. Here, we report the crystallographic study of vitamin D nuclear receptor (VDR) ligand binding domain in complexes with six nonsecosteroidal analogues harboring two or three phenyl rings. These compounds induce a stimulated transcription in the nanomolar range, similar to calcitriol. Examination of the protein-ligand interactions reveals the mode of binding of these nonsecosteroidal compounds and highlights the role of the various chemical modifications of the ligands to VDR binding and activity, notably (de)solvation effects. The structures with the tris-aromatic ligands exhibit a rearrangement of a novel region of the VDR ligand binding pocket, helix H6.

-	~~==Function==~~	+	Structural Basis for the Accommodation of Bis- and Tris-Aromatic Derivatives in Vitamin D Nuclear Receptor.,Ciesielski F, Sato Y, Chebaro Y, Moras D, Dejaegere A, Rochel N J Med Chem. 2012 Sep 19. PMID:22957834<ref>PMID:22957834</ref>
-	~~[[http://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates~~ the ~~action~~ of ~~vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin~~-~~remodeling complex. Plays a central role~~ in ~~calcium homeostasis.<ref>PMID:17218092</ref> [[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]]~~ Nuclear ~~receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion~~. ~~Involved in the coactivation of different nuclear receptors~~, ~~such as for steroids (PGR~~, ~~GR and ER)~~, ~~retinoids (RXRs)~~, ~~thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3~~, ~~STAT5A~~, ~~STAT5B and STAT6 transcription factors~~. ~~Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear~~. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:~~9427757</ref>~~<ref>PMID:~~7481822~~</ref>~~<ref>PMID:9223431</ref><ref>PMID:9296499</ref><ref>PMID:9223281</ref><ref>PMID:10449719</ref><ref>PMID:12954634</ref>~~	+
-		+
-	~~==About this Structure==~~	+
-	[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA].	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Danio rerio]]		[[Category: Danio rerio]]
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
-	[[Category: Ciesielski, F.]]	+	[[Category: Ciesielski, F]]
-	[[Category: Moras, D.]]	+	[[Category: Moras, D]]
-	[[Category: Rochel, N.]]	+	[[Category: Rochel, N]]
-	[[Category: Sato, Y.]]	+	[[Category: Sato, Y]]
	[[Category: Alpha helical sandwich]]		[[Category: Alpha helical sandwich]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 09:16, 24 March 2013

OCA — Sun, 24 Mar 2013 09:16:43 GMT

←Older revision		Revision as of 09:16, 24 March 2013
Line 1:		Line 1:
-	[[Image:4g1z.png\|left\|200px]]
-
	{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}		{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}
-
	===Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor===		===Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor===
-
	{{ABSTRACT_PUBMED_22957834}}		{{ABSTRACT_PUBMED_22957834}}
		+
		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/VDRA_DANRE VDRA_DANRE]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Plays a central role in calcium homeostasis.<ref>PMID:17218092</ref> [[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref><ref>PMID:7481822</ref><ref>PMID:9223431</ref><ref>PMID:9296499</ref><ref>PMID:9223281</ref><ref>PMID:10449719</ref><ref>PMID:12954634</ref>

	==About this Structure==		==About this Structure==
	[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA].		[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
	[[Category: Danio rerio]]		[[Category: Danio rerio]]
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]

OCA at 09:56, 21 November 2012

OCA — Wed, 21 Nov 2012 09:56:24 GMT

←Older revision		Revision as of 09:56, 21 November 2012
Line 1:		Line 1:
-	[[Image:4g1z.~~jpg~~\|left\|200px]]	+	[[Image:4g1z.png\|left\|200px]]

	{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}		{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}

OCA at 20:29, 26 September 2012

OCA — Wed, 26 Sep 2012 20:29:09 GMT

←Older revision		Revision as of 20:29, 26 September 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4g1z.jpg\|left\|200px]]

-	~~The entry~~ 4g1z ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4g1z\| PDB=4g1z \| SCENE= }}

-	~~Authors: Ciesielski, F., Sato, Y., Moras,~~ D~~., Rochel, N.~~	+	===Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor===

-	~~Description~~: ~~Structural basis for the accommodation of bis~~-~~and tris-aromatic derivatives in Vitamin~~ D Nuclear ~~Receptor~~	+	{{ABSTRACT_PUBMED_22957834}}
		+
		+	==About this Structure==
		+	[[4g1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4G1Z OCA].
		+	[[Category: Danio rerio]]
		+	[[Category: Histone acetyltransferase]]
		+	[[Category: Ciesielski, F.]]
		+	[[Category: Moras, D.]]
		+	[[Category: Rochel, N.]]
		+	[[Category: Sato, Y.]]
		+	[[Category: Alpha helical sandwich]]
		+	[[Category: Dna]]
		+	[[Category: Ligand]]
		+	[[Category: Nuclear receptor]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphorylation]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcription-transcription inhibitor complex]]
		+	[[Category: Vdr]]

OCA at 06:50, 25 July 2012

OCA — Wed, 25 Jul 2012 06:50:21 GMT

←Older revision		Revision as of 06:50, 25 July 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4g1z is ON HOLD	+	The entry 4g1z is ON HOLD until Paper Publication

	Authors: Ciesielski, F., Sato, Y., Moras, D., Rochel, N.		Authors: Ciesielski, F., Sato, Y., Moras, D., Rochel, N.

	Description: Structural basis for the accommodation of bis-and tris-aromatic derivatives in Vitamin D Nuclear Receptor		Description: Structural basis for the accommodation of bis-and tris-aromatic derivatives in Vitamin D Nuclear Receptor

OCA: Protected "4g1z" [edit=sysop:move=sysop]

OCA — Wed, 18 Jul 2012 05:08:30 GMT

Protected "4g1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:08, 18 July 2012