5vab - Revision history

OCA at 13:44, 4 October 2023

OCA — Wed, 04 Oct 2023 13:44:44 GMT

←Older revision		Revision as of 13:44, 4 October 2023
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	<StructureSection load='5vab' size='340' side='right'caption='[[5vab]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5vab' size='340' side='right'caption='[[5vab]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vab]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vab]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VAB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.702Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5va6\|5va6]], [[5vac\|5vac]], [[5vah\|5vah]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5vab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vab OCA], [~~http~~://pdbe.org/5vab PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vab RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vab PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vab 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=5vab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vab OCA], [https://pdbe.org/5vab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vab RCSB], [https://www.ebi.ac.uk/pdbsum/5vab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vab ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I1N521_SOYBN I1N521_SOYBN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Glycine max]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bergamin, E]]	+	[[Category: Bergamin E]]
-	[[Category: Blais, A]]	+	[[Category: Blais A]]
-	[[Category: Brunzelle~~, J S~~]]	+	[[Category: Brunzelle JS]]
-	[[Category: Couture, J F]]	+	[[Category: Couture J-F]]
-	[[Category: Eram, M]]	+	[[Category: Eram M]]
-	[[Category: Joshi, M]]	+	[[Category: Joshi M]]
-	[[Category: Malette, J]]	+	[[Category: Malette J]]
-	[[Category: Michaels~~, S D~~]]	+	[[Category: Michaels SD]]
-	[[Category: Mongeon, V]]	+	[[Category: Mongeon V]]
-	[[Category: Sarvan, S]]	+	[[Category: Sarvan S]]
-	[[Category: Vedadi, M]]	+	[[Category: Vedadi M]]
-	[[Category: Yeung, S]]	+	[[Category: Yeung S]]
-	~~[[Category: Transferase-dna binding protein complex~~]]	+

OCA at 08:33, 30 September 2020

OCA — Wed, 30 Sep 2020 08:33:31 GMT

←Older revision		Revision as of 08:33, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of ATXR5 PHD domain in complex with histone H3==		==Crystal structure of ATXR5 PHD domain in complex with histone H3==
-	<StructureSection load='5vab' size='340' side='right' caption='[[5vab]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5vab' size='340' side='right'caption='[[5vab]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vab]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VAB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vab]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VAB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5va6\|5va6]], [[5vac\|5vac]], [[5vah\|5vah]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5va6\|5va6]], [[5vac\|5vac]], [[5vah\|5vah]]</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=5vab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vab OCA], [http://pdbe.org/5vab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vab RCSB], [http://www.ebi.ac.uk/pdbsum/5vab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vab 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=5vab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vab OCA], [http://pdbe.org/5vab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vab RCSB], [http://www.ebi.ac.uk/pdbsum/5vab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vab ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bergamin, E]]		[[Category: Bergamin, E]]
	[[Category: Blais, A]]		[[Category: Blais, A]]

OCA at 13:05, 19 April 2017

OCA — Wed, 19 Apr 2017 13:05:31 GMT

←Older revision		Revision as of 13:05, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vab is ~~ON HOLD~~	+	==Crystal structure of ATXR5 PHD domain in complex with histone H3==
		+	<StructureSection load='5vab' size='340' side='right' caption='[[5vab]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vab]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VAB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5va6\|5va6]], [[5vac\|5vac]], [[5vah\|5vah]]</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=5vab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vab OCA], [http://pdbe.org/5vab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vab RCSB], [http://www.ebi.ac.uk/pdbsum/5vab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vab ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In plants, the histone H3.1 lysine 27 (H3K27) mono-methyltransferases ARABIDOPSIS TRITHORAX RELATED PROTEIN 5 and 6 (ATXR5/6) regulate heterochromatic DNA replication and genome stability. Our initial studies showed that ATXR5/6 discriminate between histone H3 variants and preferentially methylate K27 on H3.1. In this study, we report three regulatory mechanisms contributing to the specificity of ATXR5/6. First, we show that ATXR5 preferentially methylates the R/F-K*-S/C-G/A-P/C motif with striking preference for hydrophobic and aromatic residues in positions flanking this core of five amino acids. Second, we demonstrate that post-transcriptional modifications of residues neighboring K27 that are typically associated with actively transcribed chromatin are detrimental to ATXR5 activity. Third, we show that ATXR5 PHD domain employs a narrow binding pocket to selectively recognize unmethylated K4 of histone H3. Finally, we demonstrate that deletion or mutation of the PHD domain reduces the catalytic efficiency (kcat/Km of AdoMet) of ATXR5 up to 58-fold, highlighting the multifunctional nature of ATXR5 PHD domain. Overall, our results suggest that several molecular determinants regulate ATXR5/6 methyltransferase activity and epigenetic inheritance of H3.1 K27me1 mark in plants.

-	~~Authors:~~ Bergamin, E., Sarvan, S., Malette, J., Eram~~, M.~~, Yeung, S., Mongeon, V., Joshi, M., Brunzelle~~, J.S.~~, Michaels~~, S.D.~~, Blais, A., Vedadi, M., Couture~~, J~~.-F.	+	Molecular basis for the methylation specificity of ATXR5 for histone H3.,Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF Nucleic Acids Res. 2017 Apr 5. doi: 10.1093/nar/gkx224. PMID:28383693<ref>PMID:28383693</ref>

-	~~Description: Crystal structure~~ of ~~ATXR5 PHD domain in complex with histone H3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vab" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bergamin, E]]
	[[Category: Blais, A]]		[[Category: Blais, A]]
		+	[[Category: Brunzelle, J S]]
		+	[[Category: Couture, J F]]
		+	[[Category: Eram, M]]
		+	[[Category: Joshi, M]]
		+	[[Category: Malette, J]]
		+	[[Category: Michaels, S D]]
	[[Category: Mongeon, V]]		[[Category: Mongeon, V]]
	[[Category: Sarvan, S]]		[[Category: Sarvan, S]]
-	[[Category: Malette, J]]
	[[Category: Vedadi, M]]		[[Category: Vedadi, M]]
-	[[Category: Brunzelle, J.S]]
-	[[Category: Eram, M]]
-	[[Category: Joshi, M]]
-	[[Category: Couture, J.-F]]
	[[Category: Yeung, S]]		[[Category: Yeung, S]]
-	[[Category: ~~Bergamin, E]]~~	+	[[Category: Transferase-dna binding protein complex]]
-	~~[[Category: Michaels, S.D~~]]	+

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

OCA — Wed, 05 Apr 2017 11:51:24 GMT

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

←Older revision

Revision as of 11:51, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vab is ON HOLD Authors: Bergamin, E., Sarvan, S., Malette, J., Eram, M., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais,...

OCA — Wed, 05 Apr 2017 11:51:22 GMT

New page: '''Unreleased structure''' The entry 5vab is ON HOLD Authors: Bergamin, E., Sarvan, S., Malette, J., Eram, M., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais,...

New page

'''Unreleased structure'''

The entry 5vab is ON HOLD

Authors: Bergamin, E., Sarvan, S., Malette, J., Eram, M., Yeung, S., Mongeon, V., Joshi, M., Brunzelle, J.S., Michaels, S.D., Blais, A., Vedadi, M., Couture, J.-F.

Description: Crystal structure of ATXR5 PHD domain in complex with histone H3
[[Category: Unreleased Structures]]
[[Category: Blais, A]]
[[Category: Mongeon, V]]
[[Category: Sarvan, S]]
[[Category: Malette, J]]
[[Category: Vedadi, M]]
[[Category: Brunzelle, J.S]]
[[Category: Eram, M]]
[[Category: Joshi, M]]
[[Category: Couture, J.-F]]
[[Category: Yeung, S]]
[[Category: Bergamin, E]]
[[Category: Michaels, S.D]]