5x8x - Revision history

OCA at 07:55, 22 November 2023

OCA — Wed, 22 Nov 2023 07:55:57 GMT

←Older revision		Revision as of 07:55, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5x8x' size='340' side='right'caption='[[5x8x]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5x8x' size='340' side='right'caption='[[5x8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x8x]] is a 8 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Human Human] and [http~~://en.wikipedia.org/wiki/~~Hylobates_concolor_leucogenys Hylobates concolor leucogenys~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x8x]] is a 8 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=5X8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X8X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82O:(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide'>82O</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x8w\|5x8w]], [[5x8u\|5x8u]], [[5x8s\|5x8s]], [[5x8q\|5x8q]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82O:(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide'>82O</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RORC, NR1F3, RORG, RZRG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61853 Hylobates concolor leucogenys]), NCOR2, CTG26 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8x OCA], [https://pdbe.org/5x8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x8x RCSB], [https://www.ebi.ac.uk/pdbsum/5x8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8x ProSAT]</span></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=5x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8x OCA], [~~http~~://pdbe.org/5x8x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x8x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x8x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RORG_HUMAN RORG_HUMAN~~]] Possible nuclear receptor for hydroxycholesterols, the binding of which strongly promotes coactivators recruitment. Essential for thymopoiesis and the development of several secondary lymphoid tissues, including lymph nodes. Involved in lineage specification of uncommitted CD4(+) T-helper cells into Th17 cells. Regulate the expression of several components of the circadian clock. [[http://www.uniprot.org/uniprot/NCOR2_HUMAN NCOR2_HUMAN]] Transcriptional corepressor of NR4A2/NURR1 and acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state (By similarity). Mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Isoform 1 and isoform 5 have different affinities for different nuclear receptors.	+	[https://www.uniprot.org/uniprot/G1RH57_NOMLE G1RH57_NOMLE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Hylobates concolor leucogenys~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adachi, T]]	+	[[Category: Adachi T]]
-	[[Category: Doi, S]]	+	[[Category: Doi S]]
-	[[Category: Murase, K]]	+	[[Category: Murase K]]
-	[[Category: Noguchi, M]]	+	[[Category: Noguchi M]]
-	[[Category: Nomura, A]]	+	[[Category: Nomura A]]
-	[[Category: Yamaguchi, K]]	+	[[Category: Yamaguchi K]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Nuclear receptor]]~~	+
-	~~[[Category: Ternary complex]]~~	+
-	~~[[Category: Transferase-inhibitor complex~~]]	+

OCA at 10:31, 17 June 2020

OCA — Wed, 17 Jun 2020 10:31:00 GMT

←Older revision		Revision as of 10:31, 17 June 2020
Line 1:		Line 1:

	==Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.==		==Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.==
-	<StructureSection load='5x8x' size='340' side='right' caption='[[5x8x]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5x8x' size='340' side='right'caption='[[5x8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x8x]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X8X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x8x]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Hylobates_concolor_leucogenys Hylobates concolor leucogenys]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X8X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82O:(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide'>82O</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82O:(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide'>82O</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x8w\|5x8w]], [[5x8u\|5x8u]], [[5x8s\|5x8s]], [[5x8q\|5x8q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x8w\|5x8w]], [[5x8u\|5x8u]], [[5x8s\|5x8s]], [[5x8q\|5x8q]]</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=5x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8x OCA], [http://pdbe.org/5x8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x8x RCSB], [http://www.ebi.ac.uk/pdbsum/5x8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8x ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RORC, NR1F3, RORG, RZRG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61853 Hylobates concolor leucogenys]), NCOR2, CTG26 ([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=5x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8x OCA], [http://pdbe.org/5x8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x8x RCSB], [http://www.ebi.ac.uk/pdbsum/5x8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/NCOR2_HUMAN NCOR2_HUMAN]] Transcriptional corepressor of NR4A2/NURR1 and acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state (By similarity). Mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Isoform 1 and isoform 5 have different affinities for different nuclear receptors.	+	[[http://www.uniprot.org/uniprot/RORG_HUMAN RORG_HUMAN]] Possible nuclear receptor for hydroxycholesterols, the binding of which strongly promotes coactivators recruitment. Essential for thymopoiesis and the development of several secondary lymphoid tissues, including lymph nodes. Involved in lineage specification of uncommitted CD4(+) T-helper cells into Th17 cells. Regulate the expression of several components of the circadian clock. [[http://www.uniprot.org/uniprot/NCOR2_HUMAN NCOR2_HUMAN]] Transcriptional corepressor of NR4A2/NURR1 and acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state (By similarity). Mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Isoform 1 and isoform 5 have different affinities for different nuclear receptors.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5x8x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x8x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nuclear receptor corepressor\|Nuclear receptor corepressor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Hylobates concolor leucogenys]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, T]]		[[Category: Adachi, T]]
	[[Category: Doi, S]]		[[Category: Doi, S]]

OCA at 09:48, 3 August 2017

OCA — Thu, 03 Aug 2017 09:48:23 GMT

←Older revision		Revision as of 09:48, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x8x is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.==
		+	<StructureSection load='5x8x' size='340' side='right' caption='[[5x8x]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x8x]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X8X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82O:(3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide'>82O</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x8w\|5x8w]], [[5x8u\|5x8u]], [[5x8s\|5x8s]], [[5x8q\|5x8q]]</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=5x8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8x OCA], [http://pdbe.org/5x8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x8x RCSB], [http://www.ebi.ac.uk/pdbsum/5x8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NCOR2_HUMAN NCOR2_HUMAN]] Transcriptional corepressor of NR4A2/NURR1 and acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state (By similarity). Mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Isoform 1 and isoform 5 have different affinities for different nuclear receptors.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Retinoid-related orphan receptor gamma (RORgamma) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORgamma, we have determined the first crystal structure of a ternary complex containing RORgamma ligand-binding domain (LBD) bound with a novel synthetic inhibitor and a repressor peptide, 22-mer peptide from silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Comparison of a binary complex of nonliganded (apo) RORgamma-LBD with a nuclear receptor co-activator (NCoA-1) peptide has shown that our inhibitor displays a unique mechanism different from those caused by natural inhibitor, ursolic acid (UA). The compound unprecedentedly induces indirect disruption of a hydrogen bond between His479 on helix 11 (H11) and Tyr502 on H12, which is crucial for active conformation. This crystallographic study will allow us to develop novel synthetic compounds for autoimmune disease therapy.

-	~~Authors: Noguchi~~, M., ~~Nomura~~, A., Murase, K., Doi, S., Yamaguchi, K., ~~Adachi~~, T.	+	Ternary complex of human RORgamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment.,Noguchi M, Nomura A, Murase K, Doi S, Yamaguchi K, Hirata K, Shiozaki M, Hirashima S, Kotoku M, Yamaguchi T, Katsuda Y, Steensma R, Li X, Tao H, Tse B, Fenn M, Babine R, Bradley E, Crowe P, Thacher S, Adachi T, Kamada M Genes Cells. 2017 Jun;22(6):535-551. doi: 10.1111/gtc.12494. Epub 2017 May 11. PMID:28493531<ref>PMID:28493531</ref>

-	~~Description: Crystal Structure~~ of the ~~mutant Human ROR gamma Ligand Binding Domain With Compound A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5x8x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adachi, T]]
	[[Category: Doi, S]]		[[Category: Doi, S]]
-	[[Category: Nomura, A]]
	[[Category: Murase, K]]		[[Category: Murase, K]]
-	[[Category: Adachi, T]]
	[[Category: Noguchi, M]]		[[Category: Noguchi, M]]
		+	[[Category: Nomura, A]]
	[[Category: Yamaguchi, K]]		[[Category: Yamaguchi, K]]
		+	[[Category: Inhibitor]]
		+	[[Category: Nuclear receptor]]
		+	[[Category: Ternary complex]]
		+	[[Category: Transferase-inhibitor complex]]

OCA at 12:22, 5 April 2017

OCA — Wed, 05 Apr 2017 12:22:10 GMT

←Older revision		Revision as of 12:22, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x8x is ON HOLD	+	The entry 5x8x is ON HOLD until Paper Publication

-	Authors: ~~Masato~~ Noguchi, ~~Akihiro~~ Nomura, ~~Ken~~ Murase, ~~Satoki~~ Doi, ~~Keishi~~ Yamaguchi, ~~Tsuyoshi~~ Adachi	+	Authors: Noguchi, M., Nomura, A., Murase, K., Doi, S., Yamaguchi, K., Adachi, T.

	Description: Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.		Description: Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Masato Noguchi~~, ~~Akihiro~~ Nomura, ~~Ken~~ Murase, ~~Satoki Doi~~, ~~Keishi~~ Yamaguchi, ~~Tsuyoshi Adachi~~]]	+	[[Category: Doi, S]]
		+	[[Category: Nomura, A]]
		+	[[Category: Murase, K]]
		+	[[Category: Adachi, T]]
		+	[[Category: Noguchi, M]]
		+	[[Category: Yamaguchi, K]]

OCA: Protected "5x8x" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:55:12 GMT

Protected "5x8x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:55, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x8x is ON HOLD Authors: Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Tsuyoshi Adachi Description: Crystal Structure o...

OCA — Thu, 09 Mar 2017 15:55:11 GMT

New page: '''Unreleased structure''' The entry 5x8x is ON HOLD Authors: Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Tsuyoshi Adachi Description: Crystal Structure o...

New page

'''Unreleased structure'''

The entry 5x8x is ON HOLD

Authors: Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Tsuyoshi Adachi

Description: Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.
[[Category: Unreleased Structures]]
[[Category: Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Tsuyoshi Adachi]]