6v8w - Revision history

OCA at 08:06, 11 October 2023

OCA — Wed, 11 Oct 2023 08:06:08 GMT

←Older revision		Revision as of 08:06, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6v8w' size='340' side='right'caption='[[6v8w]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6v8w' size='340' side='right'caption='[[6v8w]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6v8w]] is a 52 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=6V8W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6V8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v8w]] is a 52 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V8W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 2.8Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5T3:'>5T3</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5T3:N~6~-ethyl-N~6~-propan-2-yl-L-lysine'>5T3</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CDYL2 ([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=6v8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v8w OCA], [https://pdbe.org/6v8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v8w RCSB], [https://www.ebi.ac.uk/pdbsum/6v8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v8w 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=6v8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v8w OCA], [~~http~~://pdbe.org/6v8w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6v8w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6v8w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6v8w ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CDYL2_HUMAN CDYL2_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Bountra, C]]	+	[[Category: Arrowsmith CH]]
		+	[[Category: Bountra C]]
		+	[[Category: Dong C]]
		+	[[Category: Edwards AM]]
		+	[[Category: James LI]]
		+	[[Category: Lamb KN]]
		+	[[Category: Min J]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-	~~[[Category: Dong, C]]~~	+	[[Category: Tempel W]]
-	~~[[Category: Edwards, A M]]~~	+
-	~~[[Category: James, L I]]~~	+
-	~~[[Category: Lamb, K N]]~~	+
-	~~[[Category: Min, J]]~~	+
-	[[Category: Tempel, W]]	+
-	~~[[Category: Chromodomain]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Sgc~~]]	+

OCA at 11:36, 29 July 2020

OCA — Wed, 29 Jul 2020 11:36:50 GMT

←Older revision		Revision as of 11:36, 29 July 2020
Line 1:		Line 1:

	==CDYL2 chromodomain in complex with a synthetic peptide==		==CDYL2 chromodomain in complex with a synthetic peptide==
-	<StructureSection load='6v8w' size='340' side='right'caption='[[6v8w]]' scene=''>	+	<StructureSection load='6v8w' size='340' side='right'caption='[[6v8w]], [[Resolution\|resolution]] 2.80Å' 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=6V8W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6v8w]] is a 52 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=6V8W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V8W 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=6v8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v8w OCA], [http://pdbe.org/6v8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v8w RCSB], [http://www.ebi.ac.uk/pdbsum/6v8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v8w 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=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5T3:'>5T3</scene>, <scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDYL2 ([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=6v8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v8w OCA], [http://pdbe.org/6v8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v8w RCSB], [http://www.ebi.ac.uk/pdbsum/6v8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v8w ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The CDY (chromodomain on the Y) proteins play an essential role in normal spermatogenesis and brain development. Dysregulation of their expression has been linked to male infertility and various neurological diseases. Like the chromodomains of HP1 and Polycomb, the CDY chromodomains also recognize the lysine-methylated ARKS motif embedded in histone and non-histone proteins. Interestingly, the CDY chromodomains exhibit different binding preferences for the lysine-methylated ARKS motif in different sequence contexts. Here, we present the structural basis for selective binding of CDY1 to H3K9me3 and preferential binding of CDYL2 to H3tK27me3 over H3K27me3. In addition, we use a CDYL1/2-selective compound, UNC4850, to gain further insight into the molecular mechanisms underlying CDYL2 binding specificity. Our work also provides critical implications that CDYL1b's role in the regulation of neural development is dependent on its recognition of the lysine-methylated ARKS motif.
		+
		+	Structural Basis for the Binding Selectivity of Human CDY Chromodomains.,Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J Cell Chem Biol. 2020 May 26. pii: S2451-9456(20)30153-7. doi:, 10.1016/j.chembiol.2020.05.007. PMID:32470319<ref>PMID:32470319</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6v8w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith CH]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bountra C]]	+	[[Category: Bountra, C]]
-	~~[[Category: Dong C]]~~	+
-	~~[[Category: Edwards AM]]~~	+
-	~~[[Category: James LI]]~~	+
-	~~[[Category: Lamb KN]]~~	+
-	~~[[Category: Min J~~]]	+
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-	[[Category: Tempel W]]	+	[[Category: Dong, C]]
		+	[[Category: Edwards, A M]]
		+	[[Category: James, L I]]
		+	[[Category: Lamb, K N]]
		+	[[Category: Min, J]]
		+	[[Category: Tempel, W]]
		+	[[Category: Chromodomain]]
		+	[[Category: Protein binding]]
		+	[[Category: Sgc]]

OCA at 10:45, 17 June 2020

OCA — Wed, 17 Jun 2020 10:45:49 GMT

←Older revision		Revision as of 10:45, 17 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6v8w is ~~ON HOLD~~	+	==CDYL2 chromodomain in complex with a synthetic peptide==
-		+	<StructureSection load='6v8w' size='340' side='right'caption='[[6v8w]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V8W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V8W 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=6v8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v8w OCA], [http://pdbe.org/6v8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v8w RCSB], [http://www.ebi.ac.uk/pdbsum/6v8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v8w ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arrowsmith CH]]
		+	[[Category: Bountra C]]
		+	[[Category: Dong C]]
		+	[[Category: Edwards AM]]
		+	[[Category: James LI]]
		+	[[Category: Lamb KN]]
		+	[[Category: Min J]]
		+	[[Category: Structural genomic]]
		+	[[Category: Tempel W]]

OCA: Protected "6v8w" [edit=sysop:move=sysop]

OCA — Wed, 18 Dec 2019 06:08:13 GMT

Protected "6v8w" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:08, 18 December 2019

OCA: New page: '''Unreleased structure''' The entry 6v8w is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Dec 2019 06:08:12 GMT

New page: '''Unreleased structure''' The entry 6v8w is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6v8w is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]