5yyf - Revision history

OCA at 08:40, 22 November 2023

OCA — Wed, 22 Nov 2023 08:40:16 GMT

←Older revision		Revision as of 08:40, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yyf' size='340' side='right'caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5yyf' size='340' side='right'caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yyf]] 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=5YYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yyf]] 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=5YYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YYF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FOA:2~~-~~FUROIC+ACID'>FOA</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.903Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MLLT3, AF9, YEATS3 ([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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [https://pdbe.org/5yyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [https://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf 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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [~~http~~://pdbe.org/5yyf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] A chromosomal aberration involving MLLT3 is associated with acute leukemias. Translocation t(9;11)(p22;q23) with KMT2A/MLL1. The result is a rogue activator protein.	+	[https://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN] A chromosomal aberration involving MLLT3 is associated with acute leukemias. Translocation t(9;11)(p22;q23) with KMT2A/MLL1. The result is a rogue activator protein.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.<ref>PMID:20159561</ref> <ref>PMID:20471948</ref>	+	[https://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN] Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.<ref>PMID:20159561</ref> <ref>PMID:20471948</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Li, H]]	+	[[Category: Li H]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	~~[[Category: 2-furancarboyl group]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Yeats domain~~]]	+

OCA at 10:00, 16 September 2020

OCA — Wed, 16 Sep 2020 10:00:13 GMT

←Older revision		Revision as of 10:00, 16 September 2020
Line 1:		Line 1:

-	==Crystal ~~strucutre~~ of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group==	+	==Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group==
-	<StructureSection load='5yyf' size='340' side='right' caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5yyf' size='340' side='right'caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yyf]] 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=5YYF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yyf]] 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=5YYF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YYF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MLLT3, AF9, YEATS3 ([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">MLLT3, AF9, YEATS3 ([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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [http://pdbe.org/5yyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [http://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf 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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [http://pdbe.org/5yyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [http://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Li, Y]]		[[Category: Li, Y]]

OCA at 20:50, 2 December 2018

OCA — Sun, 02 Dec 2018 20:50:02 GMT

←Older revision		Revision as of 20:50, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5yyf' size='340' side='right' caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5yyf' size='340' side='right' caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yyf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yyf]] 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=5YYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YYF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MLLT3, AF9, YEATS3 ([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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [http://pdbe.org/5yyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [http://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf ProSAT]</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=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [http://pdbe.org/5yyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [http://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.<ref>PMID:20159561</ref> <ref>PMID:20471948</ref>		[[http://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.<ref>PMID:20159561</ref> <ref>PMID:20471948</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS-Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique pi-pi-pi stacking interaction at the proteins' Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.
		+
		+	Structure-guided development of YEATS domain inhibitors by targeting pi-pi-pi stacking.,Li X, Li XM, Jiang Y, Liu Z, Cui Y, Fung KY, van der Beelen SHE, Tian G, Wan L, Shi X, Allis CD, Li H, Li Y, Li XD Nat Chem Biol. 2018 Dec;14(12):1140-1149. doi: 10.1038/s41589-018-0144-y. Epub, 2018 Oct 29. PMID:30374167<ref>PMID:30374167</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yyf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Li, Y]]		[[Category: Li, Y]]

OCA at 12:09, 7 November 2018

OCA — Wed, 07 Nov 2018 12:09:16 GMT

←Older revision		Revision as of 12:09, 7 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yyf is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal strucutre of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group==
-		+	<StructureSection load='5yyf' size='340' side='right' caption='[[5yyf]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yyf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YYF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOA:2-FUROIC+ACID'>FOA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=PHQ:BENZYL+CHLOROCARBONATE'>PHQ</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5yyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yyf OCA], [http://pdbe.org/5yyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yyf RCSB], [http://www.ebi.ac.uk/pdbsum/5yyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yyf ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] A chromosomal aberration involving MLLT3 is associated with acute leukemias. Translocation t(9;11)(p22;q23) with KMT2A/MLL1. The result is a rogue activator protein.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AF9_HUMAN AF9_HUMAN]] Component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA.<ref>PMID:20159561</ref> <ref>PMID:20471948</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, H]]
		+	[[Category: Li, Y]]
		+	[[Category: 2-furancarboyl group]]
		+	[[Category: Complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Transcription]]
		+	[[Category: Yeats domain]]

OCA at 17:09, 24 January 2018

OCA — Wed, 24 Jan 2018 17:09:39 GMT

←Older revision		Revision as of 17:09, 24 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 20 Dec 2017 04:50:54 GMT

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

←Older revision

Revision as of 04:50, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yyf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Dec 2017 04:50:53 GMT

New page: '''Unreleased structure''' The entry 5yyf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yyf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]