4iur - Revision history

OCA at 15:31, 20 September 2023

OCA — Wed, 20 Sep 2023 15:31:21 GMT

←Older revision		Revision as of 15:31, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4iur]] is a 3 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=4IUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4iur]] is a 3 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=4IUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <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]] 2.501Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=4iur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iur OCA], [https://pdbe.org/4iur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iur RCSB], [https://www.ebi.ac.uk/pdbsum/4iur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iur 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=4iur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iur OCA], [https://pdbe.org/4iur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iur RCSB], [https://www.ebi.ac.uk/pdbsum/4iur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iur ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:13, 16 November 2022

OCA — Wed, 16 Nov 2022 21:13:02 GMT

←Older revision		Revision as of 21:13, 16 November 2022
Line 1:		Line 1:

	==crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide==		==crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide==
-	<StructureSection load='4iur' size='340' side='right' caption='[[4iur]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4iur' size='340' side='right'caption='[[4iur]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4iur]] is a 3 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=4IUR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4iur]] is a 3 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=4IUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IUR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</scene>, ~~<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=CVM:CYMAL-4'>CVM</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4iur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iur OCA], [https://pdbe.org/4iur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4iur RCSB], [https://www.ebi.ac.uk/pdbsum/4iur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4iur ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4iup\|4iup]], [[4iuq\|4iuq]], [[4iut\|4iut]], [[4iuu\|4iuu]], [[4iuv\|4iuv]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">F9L1.16, At1g15215, AT1G15215 ([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=4iur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iur OCA], [~~http~~://pdbe.org/4iur PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4iur RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4iur PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4iur ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SHH1_ARATH SHH1_ARATH] Involved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.<ref>PMID:21811420</ref> <ref>PMID:22064704</ref> <ref>PMID:23636332</ref> <ref>PMID:23637343</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
-	[[Category: ~~Du, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Patel, D~~ J]]	+	[[Category: Du J]]
-	[[Category: ~~Gene regulation]]~~	+	[[Category: Patel DJ]]
-	~~[[Category: H3k9me3]]~~	+
-	~~[[Category: Histone]]~~	+
-	~~[[Category: Mediate interaction]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Tandem tudor]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 06:50, 5 August 2016

OCA — Fri, 05 Aug 2016 06:50:13 GMT

←Older revision		Revision as of 06:50, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4iur\| PDB=4iur \| SCENE= }}
-	===crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide===
-	{{ABSTRACT_PUBMED_23636332}}

-	==~~About this Structure~~==	+	==crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide==
-	[[4iur]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUR OCA].	+	<StructureSection load='4iur' size='340' side='right' caption='[[4iur]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4iur]] is a 3 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=4IUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IUR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVM:CYMAL-4'>CVM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4iup\|4iup]], [[4iuq\|4iuq]], [[4iut\|4iut]], [[4iuu\|4iuu]], [[4iuv\|4iuv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F9L1.16, At1g15215, AT1G15215 ([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=4iur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4iur OCA], [http://pdbe.org/4iur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4iur RCSB], [http://www.ebi.ac.uk/pdbsum/4iur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4iur ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.

-	~~==Reference==~~	+	Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.,Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE Nature. 2013 May 1. doi: 10.1038/nature12178. PMID:23636332<ref>PMID:23636332</ref>
-	<ref ~~group="xtra"~~>PMID:~~023636332~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	[[Category: ~~Arabidopsis thaliana~~]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Du, J.]]	+	</div>
-	[[Category: Patel, D J.]]	+	<div class="pdbe-citations 4iur" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arath]]
		+	[[Category: Du, J]]
		+	[[Category: Patel, D J]]
	[[Category: Gene regulation]]		[[Category: Gene regulation]]
	[[Category: H3k9me3]]		[[Category: H3k9me3]]

OCA at 14:14, 10 July 2013

OCA — Wed, 10 Jul 2013 14:14:07 GMT

←Older revision		Revision as of 14:14, 10 July 2013
Line 5:		Line 5:
	==About this Structure==		==About this Structure==
	[[4iur]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUR OCA].		[[4iur]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUR OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023636332</ref><references group="xtra"/><references/>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Du, J.]]		[[Category: Du, J.]]

OCA at 06:28, 16 May 2013

OCA — Thu, 16 May 2013 06:28:04 GMT

←Older revision		Revision as of 06:28, 16 May 2013
Line 1:		Line 1:
	{{STRUCTURE_4iur\| PDB=4iur \| SCENE= }}		{{STRUCTURE_4iur\| PDB=4iur \| SCENE= }}
	===crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide===		===crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide===
		+	{{ABSTRACT_PUBMED_23636332}}

	==About this Structure==		==About this Structure==

OCA at 07:53, 2 May 2013

OCA — Thu, 02 May 2013 07:53:07 GMT

←Older revision		Revision as of 07:53, 2 May 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4iur\| PDB=4iur \| SCENE= }}
		+	===crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide===

-	~~The entry~~ 4iur is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4iur]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IUR OCA].
-	~~Authors~~: ~~Patel~~, D.J., ~~Du,~~ J.	+	[[Category: Arabidopsis thaliana]]
-		+	[[Category: Du, J.]]
-	~~Description~~: ~~crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide~~	+	[[Category: Patel, D J.]]
		+	[[Category: Gene regulation]]
		+	[[Category: H3k9me3]]
		+	[[Category: Histone]]
		+	[[Category: Mediate interaction]]
		+	[[Category: Methylation]]
		+	[[Category: Tandem tudor]]
		+	[[Category: Zinc finger]]

OCA at 12:28, 6 February 2013

OCA — Wed, 06 Feb 2013 12:28:49 GMT

←Older revision		Revision as of 12:28, 6 February 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Patel, D.J., Du, J.		Authors: Patel, D.J., Du, J.

	Description: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide		Description: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide

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

OCA — Wed, 30 Jan 2013 12:05:23 GMT

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

←Older revision

Revision as of 12:05, 30 January 2013

OCA: New page: '''Unreleased structure''' The entry 4iur is ON HOLD Authors: Patel, D.J., Du, J. Description: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide

OCA — Wed, 30 Jan 2013 12:05:22 GMT

New page: '''Unreleased structure''' The entry 4iur is ON HOLD Authors: Patel, D.J., Du, J. Description: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide

New page

'''Unreleased structure'''

The entry 4iur is ON HOLD

Authors: Patel, D.J., Du, J.

Description: crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide