6kb1 - Revision history

OCA at 10:29, 22 November 2023

OCA — Wed, 22 Nov 2023 10:29:01 GMT

←Older revision		Revision as of 10:29, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kb1' size='340' side='right'caption='[[6kb1]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='6kb1' size='340' side='right'caption='[[6kb1]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kb1]] is a 1 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=6KB1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KB1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kb1]] 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=6KB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KB1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=T4T:2-tetradecylsulfanylethanoic+acid'>T4T</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]] 1.25Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PPARA ([http~~:/~~/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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=T4T:2-tetradecylsulfanylethanoic+acid'>T4T</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kb1 OCA], [~~http~~://pdbe.org/6kb1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kb1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kb1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kb1 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=6kb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kb1 OCA], [https://pdbe.org/6kb1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kb1 RCSB], [https://www.ebi.ac.uk/pdbsum/6kb1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kb1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN]] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>	+	[https://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6kb1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kb1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peroxisome proliferator-activated receptor 3D structures\|Peroxisome proliferator-activated receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishii, I]]	+	[[Category: Ishii I]]
-	[[Category: Kamata, S]]	+	[[Category: Kamata S]]
-	[[Category: Oyama, T]]	+	[[Category: Oyama T]]
-	[[Category: Saito, K]]	+	[[Category: Saito K]]
-	[[Category: Suda, K]]	+	[[Category: Suda K]]
-	~~[[Category: Nuclear receptor]]~~	+
-	~~[[Category: Ppar]]~~	+
-	~~[[Category: Protein-ligand complex]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 08:01, 2 December 2020

OCA — Wed, 02 Dec 2020 08:01:47 GMT

←Older revision		Revision as of 08:01, 2 December 2020
Line 1:		Line 1:

	==X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA) co-crystals obtained by soaking==		==X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA) co-crystals obtained by soaking==
-	<StructureSection load='6kb1' size='340' side='right'caption='[[6kb1]]' scene=''>	+	<StructureSection load='6kb1' size='340' side='right'caption='[[6kb1]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KB1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KB1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kb1]] is a 1 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=6KB1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KB1 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kb1 OCA], [http://pdbe.org/6kb1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kb1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kb1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kb1 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=T4T:2-tetradecylsulfanylethanoic+acid'>T4T</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPARA ([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://proteopedia.org/fgij/fg.htm?mol=6kb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kb1 OCA], [http://pdbe.org/6kb1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kb1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kb1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kb1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PPARA_HUMAN PPARA_HUMAN]] Ligand-activated transcription factor. Key regulator of lipid metabolism. Activated by the endogenous ligand 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (16:0/18:1-GPC). Activated by oleylethanolamide, a naturally occurring lipid that regulates satiety (By similarity). Receptor for peroxisome proliferators such as hypolipidemic drugs and fatty acids. Regulates the peroxisomal beta-oxidation pathway of fatty acids. Functions as transcription activator for the ACOX1 and P450 genes. Transactivation activity requires heterodimerization with RXRA and is antagonized by NR2C2.<ref>PMID:7684926</ref> <ref>PMID:7629123</ref> <ref>PMID:9556573</ref> <ref>PMID:10195690</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most triacylglycerol-lowering fibrates have been developed in the 1960s-1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARalpha), was identified. Twenty-one ligand-bound PPARalpha structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARalpha ligand-binding domain, which are composed of a "Center" and four "Arm" regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARalpha agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARalpha potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARalpha ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs.
		+
		+	PPARalpha Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates.,Kamata S, Oyama T, Saito K, Honda A, Yamamoto Y, Suda K, Ishikawa R, Itoh T, Watanabe Y, Shibata T, Uchida K, Suematsu M, Ishii I iScience. 2020 Oct 23;23(11):101727. doi: 10.1016/j.isci.2020.101727. eCollection, 2020 Nov 20. PMID:33205029<ref>PMID:33205029</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kb1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishii I]]	+	[[Category: Ishii, I]]
-	[[Category: Kamata S]]	+	[[Category: Kamata, S]]
-	[[Category: Oyama T]]	+	[[Category: Oyama, T]]
-	[[Category: Saito K]]	+	[[Category: Saito, K]]
-	[[Category: Suda K]]	+	[[Category: Suda, K]]
		+	[[Category: Nuclear receptor]]
		+	[[Category: Ppar]]
		+	[[Category: Protein-ligand complex]]
		+	[[Category: Transcription]]

OCA at 07:56, 11 November 2020

OCA — Wed, 11 Nov 2020 07:56:32 GMT

←Older revision		Revision as of 07:56, 11 November 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kb1 is ~~ON HOLD until Paper Publication~~	+	==X-ray structure of human PPARalpha ligand binding domain-tetradecylthioacetic acid (TTA) co-crystals obtained by soaking==
-		+	<StructureSection load='6kb1' size='340' side='right'caption='[[6kb1]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KB1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KB1 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kb1 OCA], [http://pdbe.org/6kb1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kb1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kb1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kb1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ishii I]]
		+	[[Category: Kamata S]]
		+	[[Category: Oyama T]]
		+	[[Category: Saito K]]
		+	[[Category: Suda K]]

OCA at 04:33, 31 July 2019

OCA — Wed, 31 Jul 2019 04:33:17 GMT

←Older revision		Revision as of 04:33, 31 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kb1 is ON HOLD	+	The entry 6kb1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6kb1" [edit=sysop:move=sysop]

OCA — Wed, 03 Jul 2019 04:05:30 GMT

Protected "6kb1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kb1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 03 Jul 2019 04:05:29 GMT

New page: '''Unreleased structure''' The entry 6kb1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kb1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]