5xvl - Revision history

OCA at 10:20, 27 March 2024

OCA — Wed, 27 Mar 2024 10:20:36 GMT

←Older revision		Revision as of 10:20, 27 March 2024
Line 1:		Line 1:

	==Crystal structure of AL2 PAL domain==		==Crystal structure of AL2 PAL domain==
-	<StructureSection load='5xvl' size='340' side='right' caption='[[5xvl]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='5xvl' size='340' side='right'caption='[[5xvl]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVL 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~~></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]] 1.629Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~AL2, At3g11200, F11B9.12, F9F8.2 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~</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></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=5xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvl OCA], [~~http~~://pdbe.org/5xvl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xvl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xvl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvl 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=5xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvl OCA], [https://pdbe.org/5xvl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvl RCSB], [https://www.ebi.ac.uk/pdbsum/5xvl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALFL2_ARATH ALFL2_ARATH]] Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.	+	[https://www.uniprot.org/uniprot/ALFL2_ARATH ALFL2_ARATH] Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Polycomb group proteins play essential roles in transcriptional gene repression during both animal and plant development. Polycomb repression complex 1 (PRC1) is one of the key functional modules in polycomb group silencing. It acts as both a reader of H3K27me3 (histone H3 lysine 27 trimethylation) and a writer of H2Aub1 (histone H2A monoubiquitination) in establishing stable repression chromatin state. Intriguingly, a recent study showed that Arabidopsis PRC1 contains the H3K4me3-binding proteins of the ALFIN-like (AL) family, pointing to a chromatin state switch from active to repressive transcription of embryonic genes required for vegetative plant development. However, molecular and structural basis of AL-PRC1 complexes are lacking, which harmed insightful mechanistic understanding of AL-PRC1 complex function. In the present study, we report the crystal structures of the PAL domain (DUF3594 domain) of AL2 and AL7 proteins as well as their mechanistic binding to the PRC1 ring-finger proteins (RING1 and BMI1). We found that the PAL domain exists as a homodimer and represents a novel protein fold. We further determined the crystal structures of the PAL domain of AL2 (AL2-PAL) in complex with AtRING1a and AtBMI1b, the two core components of Arabidopsis PRC1. Interestingly, two PAL-binding sites were found on AtRING1a. Each of them can bind AL but with different affinities and distinct structural bases. Based on our results, we propose a mechanistic model to understand how AL proteins target PRC1 to active chromatin to undergo the transition from H3K4me3 to H2Aub1/H3K27me3 in establishing gene silencing.	+
-		+
-	Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch.,Peng L, Wang L, Zhang Y, Dong A, Shen WH, Huang Y J Mol Biol. 2018 Oct 19;430(21):4245-4259. doi: 10.1016/j.jmb.2018.08.021. Epub, 2018 Aug 31. PMID:30176245<ref>PMID:30176245</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xvl" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: ~~Huang, Y~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Peng, L~~]]	+	[[Category: Huang Y]]
-	[[Category: ~~Wang, L~~ L]]	+	[[Category: Peng L]]
-	[[Category: ~~Alfin-like family protein]]~~	+	[[Category: Wang LL]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Prc1 interactor~~]]	+

OCA at 12:25, 16 January 2019

OCA — Wed, 16 Jan 2019 12:25:56 GMT

←Older revision		Revision as of 12:25, 16 January 2019
Line 3:		Line 3:
	<StructureSection load='5xvl' size='340' side='right' caption='[[5xvl]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='5xvl' size='340' side='right' caption='[[5xvl]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVL 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AL2, At3g11200, F11B9.12, F9F8.2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=5xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvl OCA], [http://pdbe.org/5xvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvl RCSB], [http://www.ebi.ac.uk/pdbsum/5xvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvl 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=5xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvl OCA], [http://pdbe.org/5xvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvl RCSB], [http://www.ebi.ac.uk/pdbsum/5xvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ALFL2_ARATH ALFL2_ARATH]] Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.		[[http://www.uniprot.org/uniprot/ALFL2_ARATH ALFL2_ARATH]] Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polycomb group proteins play essential roles in transcriptional gene repression during both animal and plant development. Polycomb repression complex 1 (PRC1) is one of the key functional modules in polycomb group silencing. It acts as both a reader of H3K27me3 (histone H3 lysine 27 trimethylation) and a writer of H2Aub1 (histone H2A monoubiquitination) in establishing stable repression chromatin state. Intriguingly, a recent study showed that Arabidopsis PRC1 contains the H3K4me3-binding proteins of the ALFIN-like (AL) family, pointing to a chromatin state switch from active to repressive transcription of embryonic genes required for vegetative plant development. However, molecular and structural basis of AL-PRC1 complexes are lacking, which harmed insightful mechanistic understanding of AL-PRC1 complex function. In the present study, we report the crystal structures of the PAL domain (DUF3594 domain) of AL2 and AL7 proteins as well as their mechanistic binding to the PRC1 ring-finger proteins (RING1 and BMI1). We found that the PAL domain exists as a homodimer and represents a novel protein fold. We further determined the crystal structures of the PAL domain of AL2 (AL2-PAL) in complex with AtRING1a and AtBMI1b, the two core components of Arabidopsis PRC1. Interestingly, two PAL-binding sites were found on AtRING1a. Each of them can bind AL but with different affinities and distinct structural bases. Based on our results, we propose a mechanistic model to understand how AL proteins target PRC1 to active chromatin to undergo the transition from H3K4me3 to H2Aub1/H3K27me3 in establishing gene silencing.
		+
		+	Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch.,Peng L, Wang L, Zhang Y, Dong A, Shen WH, Huang Y J Mol Biol. 2018 Oct 19;430(21):4245-4259. doi: 10.1016/j.jmb.2018.08.021. Epub, 2018 Aug 31. PMID:30176245<ref>PMID:30176245</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xvl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Huang, Y]]		[[Category: Huang, Y]]
	[[Category: Peng, L]]		[[Category: Peng, L]]

OCA at 07:07, 4 July 2018

OCA — Wed, 04 Jul 2018 07:07:46 GMT

←Older revision		Revision as of 07:07, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xvl is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of AL2 PAL domain==
-		+	<StructureSection load='5xvl' size='340' side='right' caption='[[5xvl]], [[Resolution\|resolution]] 1.63Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xvl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVL FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5xvl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvl OCA], [http://pdbe.org/5xvl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvl RCSB], [http://www.ebi.ac.uk/pdbsum/5xvl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALFL2_ARATH ALFL2_ARATH]] Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Huang, Y]]
		+	[[Category: Peng, L]]
		+	[[Category: Wang, L L]]
		+	[[Category: Alfin-like family protein]]
		+	[[Category: Gene regulation]]
		+	[[Category: Prc1 interactor]]

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

OCA — Wed, 27 Sep 2017 15:49:48 GMT

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

←Older revision

Revision as of 15:49, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xvl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 15:49:47 GMT

New page: '''Unreleased structure''' The entry 5xvl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xvl is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]