3qby - Revision history

OCA at 11:40, 14 March 2024

OCA — Thu, 14 Mar 2024 11:40:16 GMT

←Older revision		Revision as of 11:40, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3qby' size='340' side='right'caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3qby' size='340' side='right'caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qby]] is a 4 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=3QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~, ~~<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]] 1.95Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">HDGFRP2, HDGF2, UNQ785/PRO1604 ([https://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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [https://pdbe.org/3qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [https://www.ebi.ac.uk/pdbsum/3qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qby 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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [https://pdbe.org/3qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [https://www.ebi.ac.uk/pdbsum/3qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qby ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/HDGR2_HUMAN HDGR2_HUMAN]
-	~~BACKGROUND~~: The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. METHODOLOGY/PRINCIPAL FINDINGS: The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. CONCLUSIONS: PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical beta-barrel core, an insertion motif between the second and third beta-strands and a C-terminal alpha-helix bundle. Both the canonical beta-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.	+
-		+
-	Structural and Histone Binding Ability Characterizations of Human PWWP Domains.,Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545<ref>PMID:21720545</~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3qby" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adams-Cioaba~~, M A~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Amaya~~, M F~~]]	+	[[Category: Adams-Cioaba MA]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Amaya MF]]
-	[[Category: Bountra, C]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Bountra C]]
-	[[Category: Mackenzie, F]]	+	[[Category: Edwards AM]]
-	[[Category: Min, J]]	+	[[Category: Mackenzie F]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Min J]]
-	[[Category: Tempel, W]]	+	[[Category: Tempel W]]
-	[[Category: Weigelt, J]]	+	[[Category: Weigelt J]]
-	[[Category: Wu, H]]	+	[[Category: Wu H]]
-	[[Category: Zeng, H]]	+	[[Category: Zeng H]]
-	~~[[Category: Hdgf2]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Sgc~~]]	+

OCA at 06:01, 8 June 2022

OCA — Wed, 08 Jun 2022 06:01:31 GMT

←Older revision		Revision as of 06:01, 8 June 2022
Line 1:		Line 1:

	==Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2==		==Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2==
-	<StructureSection load='3qby' size='340' side='right' caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3qby' size='340' side='right'caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qby]] 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=3QBY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QBY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QBY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([~~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">HDGFRP2, HDGF2, UNQ785/PRO1604 ([https://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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [~~http~~://pdbe.org/3qby PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qby PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qby 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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [https://pdbe.org/3qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [https://www.ebi.ac.uk/pdbsum/3qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qby ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Adams-Cioaba, M A]]		[[Category: Adams-Cioaba, M A]]
	[[Category: Amaya, M F]]		[[Category: Amaya, M F]]

OCA at 14:58, 5 August 2016

OCA — Fri, 05 Aug 2016 14:58:51 GMT

←Older revision		Revision as of 14:58, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2==		==Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2==
	<StructureSection load='3qby' size='340' side='right' caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3qby' size='340' side='right' caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QBY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qby]] 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=3QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QBY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [http://www.ebi.ac.uk/pdbsum/3qby PDBsum]</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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [http://pdbe.org/3qby PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [http://www.ebi.ac.uk/pdbsum/3qby PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qby ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3qby" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Adams-Cioaba, M A]]		[[Category: Adams-Cioaba, M A]]
	[[Category: Amaya, M F]]		[[Category: Amaya, M F]]

OCA at 23:04, 3 January 2015

OCA — Sat, 03 Jan 2015 23:04:48 GMT

←Older revision		Revision as of 23:04, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QBY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QBY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [http://www.ebi.ac.uk/pdbsum/3qby PDBsum]</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=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [http://www.ebi.ac.uk/pdbsum/3qby PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Adams-Cioaba, M A.]]	+	[[Category: Adams-Cioaba, M A]]
-	[[Category: Amaya, M F.]]	+	[[Category: Amaya, M F]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bountra, C.]]	+	[[Category: Bountra, C]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Mackenzie, F.]]	+	[[Category: Mackenzie, F]]
-	[[Category: Min, J.]]	+	[[Category: Min, J]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Tempel, W.]]	+	[[Category: Tempel, W]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
-	[[Category: Wu, H.]]	+	[[Category: Wu, H]]
-	[[Category: Zeng, H.]]	+	[[Category: Zeng, H]]
	[[Category: Hdgf2]]		[[Category: Hdgf2]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomics consortium]]

OCA at 06:49, 25 June 2014

OCA — Wed, 25 Jun 2014 06:49:17 GMT

←Older revision		Revision as of 06:49, 25 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3qby.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2==
		+	<StructureSection load='3qby' size='340' side='right' caption='[[3qby]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QBY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HDGFRP2, HDGF2, UNQ785/PRO1604 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qby OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qby RCSB], [http://www.ebi.ac.uk/pdbsum/3qby PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. METHODOLOGY/PRINCIPAL FINDINGS: The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. CONCLUSIONS: PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical beta-barrel core, an insertion motif between the second and third beta-strands and a C-terminal alpha-helix bundle. Both the canonical beta-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones. ENHANCED VERSION: This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

-	~~{{STRUCTURE_3qby\| PDB=3qby \| SCENE= }}~~	+	Structural and Histone Binding Ability Characterizations of Human PWWP Domains.,Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J PLoS One. 2011;6(6):e18919. Epub 2011 Jun 20. PMID:21720545<ref>PMID:21720545</ref>

-	~~===Crystal structure~~ of the ~~PWWP domain of human Hepatoma-derived growth factor 2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21720545}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3qby]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021720545<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Adams-Cioaba, M A.]]		[[Category: Adams-Cioaba, M A.]]

OCA at 05:46, 5 September 2012

OCA — Wed, 05 Sep 2012 05:46:42 GMT

←Older revision		Revision as of 05:46, 5 September 2012
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	[[Image:3qby.png\|left\|200px]]		[[Image:3qby.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qby", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qby\| PDB=3qby \| SCENE= }}		{{STRUCTURE_3qby\| PDB=3qby \| SCENE= }}

	===Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2===		===Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21720545}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21720545 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_21720545}}		{{ABSTRACT_PUBMED_21720545}}

OCA at 05:24, 20 July 2011

OCA — Wed, 20 Jul 2011 05:24:33 GMT

←Older revision		Revision as of 05:24, 20 July 2011
Line 1:		Line 1:
-	[[Image:3qby.~~jpg~~\|left\|200px]]	+	[[Image:3qby.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2===		===Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21720545}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21720545 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21720545}}

	==About this Structure==		==About this Structure==
	[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA].		[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021720545</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Adams-Cioaba, M A.]]		[[Category: Adams-Cioaba, M A.]]
Line 27:		Line 36:
	[[Category: Wu, H.]]		[[Category: Wu, H.]]
	[[Category: Zeng, H.]]		[[Category: Zeng, H.]]
		+	[[Category: Hdgf2]]
		+	[[Category: Protein binding]]
		+	[[Category: Sgc]]
		+	[[Category: Structural genomics consortium]]

OCA at 06:14, 9 February 2011

OCA — Wed, 09 Feb 2011 06:14:56 GMT

←Older revision		Revision as of 06:14, 9 February 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3qby.jpg\|left\|200px]]

-	The ~~entry 3qby~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qby", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qby\| PDB=3qby \| SCENE= }}

-	~~Authors: Zeng, H., Tempel, W., Amaya, M.F., Adams~~-~~Cioaba, M.A., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)~~	+	===Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2===

-	~~Description: Crystal~~ structure ~~of the PWWP domain of human Hepatoma~~-~~derived growth factor 2~~	+
		+	==About this Structure==
		+	[[3qby]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QBY OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Adams-Cioaba, M A.]]
		+	[[Category: Amaya, M F.]]
		+	[[Category: Arrowsmith, C H.]]
		+	[[Category: Bountra, C.]]
		+	[[Category: Edwards, A M.]]
		+	[[Category: Mackenzie, F.]]
		+	[[Category: Min, J.]]
		+	[[Category: SGC, Structural Genomics Consortium.]]
		+	[[Category: Tempel, W.]]
		+	[[Category: Weigelt, J.]]
		+	[[Category: Wu, H.]]
		+	[[Category: Zeng, H.]]

OCA at 06:10, 2 February 2011

OCA — Wed, 02 Feb 2011 06:10:13 GMT

←Older revision		Revision as of 06:10, 2 February 2011
Line 3:		Line 3:
	The entry 3qby is ON HOLD		The entry 3qby is ON HOLD

-	Authors: Zeng, H., Tempel, W., Amaya, M. F., Adams-Cioaba, M.A., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C. H., Edwards, A. M., Min, J., Wu, H., Structural Genomics Consortium (SGC)	+	Authors: Zeng, H., Tempel, W., Amaya, M.F., Adams-Cioaba, M.A., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

	Description: Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2		Description: Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2

OCA: Protected "3qby" [edit=sysop:move=sysop]

OCA — Wed, 26 Jan 2011 12:45:43 GMT

Protected "3qby" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 26 January 2011