4yyk - Revision history

OCA at 08:09, 27 September 2023

OCA — Wed, 27 Sep 2023 08:09:58 GMT

←Older revision		Revision as of 08:09, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yyk]] is a 6 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=4YYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YYK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yyk]] is a 6 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=4YYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YYK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</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]] 1.79Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [https://pdbe.org/4yyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [https://www.ebi.ac.uk/pdbsum/4yyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyk 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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [https://pdbe.org/4yyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [https://www.ebi.ac.uk/pdbsum/4yyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:31, 10 May 2023

OCA — Wed, 10 May 2023 07:31:15 GMT

←Older revision		Revision as of 07:31, 10 May 2023
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	==Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide==		==Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide==
-	<StructureSection load='4yyk' size='340' side='right' caption='[[4yyk]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='4yyk' size='340' side='right'caption='[[4yyk]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yyk]] is a 6 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=4YYK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yyk]] is a 6 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=4YYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YYK FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yy4\|4yy4]], [[4yy6\|4yy6]], [[4yyd\|4yyd]], [[4yyg\|4yyg]], [[4yyh\|4yyh]], [[4yyi\|4yyi]], [[4yyj\|4yyj]], [[4yym\|4yym]], [[4yyn\|4yyn]]</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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [https://pdbe.org/4yyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [https://www.ebi.ac.uk/pdbsum/4yyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyk ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD9, UNQ3040/PRO9856 ([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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [~~http~~://pdbe.org/4yyk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yyk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN]] May play a role in chromatin remodeling and regulation of transcription.	+	[https://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN] May play a role in chromatin remodeling and regulation of transcription.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4yyk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yyk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein 3D structures\|Bromodomain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Bellon, S]]	+	[[Category: Large Structures]]
-	[[Category: Cochran~~, A G~~]]	+	[[Category: Bellon S]]
-	[[Category: Poy, F]]	+	[[Category: Cochran AG]]
-	[[Category: Tang, Y]]	+	[[Category: Poy F]]
-	~~[[Category: Bromodomain-crotonyllysine complex]]~~	+	[[Category: Tang Y]]
-	~~[[Category: Protein binding~~]]	+

OCA at 17:06, 16 November 2017

OCA — Thu, 16 Nov 2017 17:06:08 GMT

←Older revision		Revision as of 17:06, 16 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide==		==Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide==
	<StructureSection load='4yyk' size='340' side='right' caption='[[4yyk]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='4yyk' size='340' side='right' caption='[[4yyk]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yyk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YYK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yyk]] is a 6 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=4YYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YYK FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yy4\|4yy4]], [[4yy6\|4yy6]], [[4yyd\|4yyd]], [[4yyg\|4yyg]], [[4yyh\|4yyh]], [[4yyi\|4yyi]], [[4yyj\|4yyj]], [[4yym\|4yym]], [[4yyn\|4yyn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yy4\|4yy4]], [[4yy6\|4yy6]], [[4yyd\|4yyd]], [[4yyg\|4yyg]], [[4yyh\|4yyh]], [[4yyi\|4yyi]], [[4yyj\|4yyj]], [[4yym\|4yym]], [[4yyn\|4yyn]]</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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [http://pdbe.org/4yyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [http://www.ebi.ac.uk/pdbsum/4yyk PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD9, UNQ3040/PRO9856 ([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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [http://pdbe.org/4yyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [http://www.ebi.ac.uk/pdbsum/4yyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Bellon, S]]		[[Category: Bellon, S]]
	[[Category: Cochran, A G]]		[[Category: Cochran, A G]]

OCA at 06:04, 30 September 2015

OCA — Wed, 30 Sep 2015 06:04:28 GMT

←Older revision		Revision as of 06:04, 30 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide==
		+	<StructureSection load='4yyk' size='340' side='right' caption='[[4yyk]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yyk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YYK FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCR:N-6-CROTONYL-L-LYSINE'>KCR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yy4\|4yy4]], [[4yy6\|4yy6]], [[4yyd\|4yyd]], [[4yyg\|4yyg]], [[4yyh\|4yyh]], [[4yyi\|4yyi]], [[4yyj\|4yyj]], [[4yym\|4yym]], [[4yyn\|4yyn]]</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=4yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyk OCA], [http://pdbe.org/4yyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yyk RCSB], [http://www.ebi.ac.uk/pdbsum/4yyk PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN]] May play a role in chromatin remodeling and regulation of transcription.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. None of the human bromodomains tested binds succinyl marks. We characterized structurally and biochemically the binding to different acyl groups, identifying bromodomain residues and structural attributes that contribute to specificity. These studies demonstrate a surprising degree of plasticity in some human bromodomains but no single factor controlling specificity across the family. The identification of candidate butyryl- and crotonyllysine readers supports the idea that these marks could have specific physiological functions.

-	~~The entry 4yyk is ON HOLD until Paper Publication~~	+	A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.,Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG Structure. 2015 Sep 4. pii: S0969-2126(15)00329-9. doi:, 10.1016/j.str.2015.08.004. PMID:26365797<ref>PMID:26365797</ref>

-	~~Authors: Tang~~, Y.~~, Bellon,~~ S.~~, Cochran, A.G., Poy, F~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 4yyk" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Cochran, A.G]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bellon, S]]
		+	[[Category: Cochran, A G]]
	[[Category: Poy, F]]		[[Category: Poy, F]]
-	[[Category: Bellon, S]]
	[[Category: Tang, Y]]		[[Category: Tang, Y]]
		+	[[Category: Bromodomain-crotonyllysine complex]]
		+	[[Category: Protein binding]]

OCA at 10:18, 13 May 2015

OCA — Wed, 13 May 2015 10:18:51 GMT

←Older revision		Revision as of 10:18, 13 May 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Tang, Y., Bellon, S., Cochran, A.G., Poy, F.		Authors: Tang, Y., Bellon, S., Cochran, A.G., Poy, F.

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

OCA — Wed, 01 Apr 2015 12:03:27 GMT

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

←Older revision

Revision as of 12:03, 1 April 2015

OCA: New page: '''Unreleased structure''' The entry 4yyk is ON HOLD Authors: Tang, Y., Bellon, S., Cochran, A.G., Poy, F. Description: Category: Unreleased Structures Category: Cochran, A.G ...

OCA — Wed, 01 Apr 2015 12:03:25 GMT

New page: '''Unreleased structure''' The entry 4yyk is ON HOLD Authors: Tang, Y., Bellon, S., Cochran, A.G., Poy, F. Description: Category: Unreleased Structures Category: Cochran, A.G ...

New page

'''Unreleased structure'''

The entry 4yyk is ON HOLD

Authors: Tang, Y., Bellon, S., Cochran, A.G., Poy, F.

Description:
[[Category: Unreleased Structures]]
[[Category: Cochran, A.G]]
[[Category: Poy, F]]
[[Category: Bellon, S]]
[[Category: Tang, Y]]