6mnm - Revision history

OCA at 06:35, 11 October 2023

2023-10-11T06:35:05Z

←Older revision		Revision as of 06:35, 11 October 2023
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	<StructureSection load='6mnm' size='340' side='right'caption='[[6mnm]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6mnm' size='340' side='right'caption='[[6mnm]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mnm]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MNM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MNM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mnm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MNM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MNM FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>H2-Aa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=10090 LK3 transgenic mice]), H2-Ab1, H2-iabeta ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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]] 3.1Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein~~-~~arginine_deiminase Protein-arginine deiminase]~~, ~~with EC number~~ [~~http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~3.~~5.3.15 3.5.3.15] </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=6mnm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mnm OCA], [https://pdbe.org/6mnm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mnm RCSB], [https://www.ebi.ac.uk/pdbsum/6mnm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mnm 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=6mnm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mnm OCA], [~~http~~://pdbe.org/6mnm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mnm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mnm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mnm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~PADI4_MOUSE PADI4_MOUSE~~]] Catalyzes the citrullination/deimination of arginine residues of proteins such as histones, thereby playing a key role in histone code and regulation of stem cell maintenance. Citrullinates histone H1 at 'Arg-54' (to form H1R54ci), histone H3 at 'Arg-2', 'Arg-8', 'Arg-17' and/or 'Arg-26' (to form H3R2ci, H3R8ci, H3R17ci, H3R26ci, respectively) and histone H4 at 'Arg-3' (to form H4R3ci). Acts as a key regulator of stem cell maintenance by mediating citrullination of histone H1: citrullination of 'Arg-54' of histone H1 (H1R54ci) results in H1 displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance. Promotes profound chromatin decondensation during the innate immune response to infection in neutrophils by mediating formation of H1R54ci. Citrullination of histone H3 prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1.<ref>PMID:15339660</ref> <ref>PMID:20733033</ref> <ref>PMID:23650392</ref> <ref>PMID:24463520</ref>	+	[https://www.uniprot.org/uniprot/HA2B_MOUSE HA2B_MOUSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6mnm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6mnm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[MHC 3D structures\|MHC 3D structures]]
		+	*[[MHC II 3D structures\|MHC II 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice]]~~	+	[[Category: Mus musculus]]
-	~~[[Category: Protein-arginine deiminase~~]]	+	[[Category: Blevins SJ]]
-	[[Category: Blevins~~, S J~~]]	+	[[Category: Huseby ES]]
-	[[Category: Huseby~~, E S~~]]	+	[[Category: Stadinski BD]]
-	[[Category: Stadinski~~, B D]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Major histocompatibility complex]]~~	+
-	~~[[Category: T cell receptor~~]]	+

OCA at 06:59, 31 July 2019

2019-07-31T06:59:13Z

←Older revision		Revision as of 06:59, 31 July 2019
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	<StructureSection load='6mnm' size='340' side='right'caption='[[6mnm]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='6mnm' size='340' side='right'caption='[[6mnm]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mnm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MNM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MNM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mnm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MNM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MNM FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-arginine_deiminase Protein-arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.15 3.5.3.15] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H2-Aa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), H2-Ab1, H2-iabeta ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-arginine_deiminase Protein-arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.15 3.5.3.15] </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=6mnm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mnm OCA], [http://pdbe.org/6mnm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mnm RCSB], [http://www.ebi.ac.uk/pdbsum/6mnm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mnm 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=6mnm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mnm OCA], [http://pdbe.org/6mnm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mnm RCSB], [http://www.ebi.ac.uk/pdbsum/6mnm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mnm ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Protein-arginine deiminase]]		[[Category: Protein-arginine deiminase]]
	[[Category: Blevins, S J]]		[[Category: Blevins, S J]]

OCA at 05:53, 3 July 2019

2019-07-03T05:53:48Z

←Older revision		Revision as of 05:53, 3 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6mnm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==6256 TCR bound to I-Ab Padi4==
		+	<StructureSection load='6mnm' size='340' side='right'caption='[[6mnm]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mnm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MNM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MNM FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-arginine_deiminase Protein-arginine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.15 3.5.3.15] </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=6mnm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mnm OCA], [http://pdbe.org/6mnm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mnm RCSB], [http://www.ebi.ac.uk/pdbsum/6mnm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mnm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PADI4_MOUSE PADI4_MOUSE]] Catalyzes the citrullination/deimination of arginine residues of proteins such as histones, thereby playing a key role in histone code and regulation of stem cell maintenance. Citrullinates histone H1 at 'Arg-54' (to form H1R54ci), histone H3 at 'Arg-2', 'Arg-8', 'Arg-17' and/or 'Arg-26' (to form H3R2ci, H3R8ci, H3R17ci, H3R26ci, respectively) and histone H4 at 'Arg-3' (to form H4R3ci). Acts as a key regulator of stem cell maintenance by mediating citrullination of histone H1: citrullination of 'Arg-54' of histone H1 (H1R54ci) results in H1 displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance. Promotes profound chromatin decondensation during the innate immune response to infection in neutrophils by mediating formation of H1R54ci. Citrullination of histone H3 prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1.<ref>PMID:15339660</ref> <ref>PMID:20733033</ref> <ref>PMID:23650392</ref> <ref>PMID:24463520</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The neonatal thymus generates Foxp3(+) regulatory T (tTreg) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tTreg cell selection is unresolved. Here we identify 17 self-peptides recognized by neonatal tTreg cells, and reveal ligand specificity patterns that include self-antigens presented in an age- and inflammation-dependent manner. Fate-mapping studies of neonatal peptidyl arginine deiminase type IV (Padi4)-specific thymocytes reveal disparate fate choices. Neonatal thymocytes expressing T cell receptors that engage IA(b)-Padi4 with moderate dwell times within a conventional docking orientation are exported as tTreg cells. In contrast, Padi4-specific T cell receptors with short dwell times are expressed on CD4(+) T cells, while long dwell times induce negative selection. Temporally, Padi4-specific thymocytes are subject to a developmental stage-specific change in negative selection, which precludes tTreg cell development. Thus, a temporal switch in negative selection and ligand binding kinetics constrains the neonatal tTreg selection window.

-	~~Authors: Blevins, S.J~~., Stadinski, ~~B.D.~~, Huseby, E.S.	+	A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3(+) Treg cell development.,Stadinski BD, Blevins SJ, Spidale NA, Duke BR, Huseby PG, Stern LJ, Huseby ES Nat Immunol. 2019 Jun 17. pii: 10.1038/s41590-019-0414-1. doi:, 10.1038/s41590-019-0414-1. PMID:31209405<ref>PMID:31209405</ref>

-	~~Description: 6256 TCR bound to I~~-~~Ab Padi4~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Stadinski~~, ~~B.D~~]]	+	<div class="pdbe-citations 6mnm" style="background-color:#fffaf0;"></div>
-	[[Category: Huseby, E.S]]	+	== References ==
-	[[Category: ~~Blevins~~, ~~S.J~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Protein-arginine deiminase]]
		+	[[Category: Blevins, S J]]
		+	[[Category: Huseby, E S]]
		+	[[Category: Stadinski, B D]]
		+	[[Category: Immune system]]
		+	[[Category: Major histocompatibility complex]]
		+	[[Category: T cell receptor]]

OCA at 06:33, 17 October 2018

2018-10-17T06:33:42Z

←Older revision		Revision as of 06:33, 17 October 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6mnm is ON HOLD	+	The entry 6mnm is ON HOLD until Paper Publication

	Authors: Blevins, S.J., Stadinski, B.D., Huseby, E.S.		Authors: Blevins, S.J., Stadinski, B.D., Huseby, E.S.
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	Description: 6256 TCR bound to I-Ab Padi4		Description: 6256 TCR bound to I-Ab Padi4
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Huseby, E.S]]
	[[Category: Stadinski, B.D]]		[[Category: Stadinski, B.D]]
		+	[[Category: Huseby, E.S]]
	[[Category: Blevins, S.J]]		[[Category: Blevins, S.J]]

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

2018-10-10T06:35:24Z

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

←Older revision

Revision as of 06:35, 10 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mnm is ON HOLD Authors: Blevins, S.J., Stadinski, B.D., Huseby, E.S. Description: 6256 TCR bound to I-Ab Padi4 Category: Unreleased Structures...

2018-10-10T06:35:23Z

New page: '''Unreleased structure''' The entry 6mnm is ON HOLD Authors: Blevins, S.J., Stadinski, B.D., Huseby, E.S. Description: 6256 TCR bound to I-Ab Padi4 Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 6mnm is ON HOLD

Authors: Blevins, S.J., Stadinski, B.D., Huseby, E.S.

Description: 6256 TCR bound to I-Ab Padi4
[[Category: Unreleased Structures]]
[[Category: Huseby, E.S]]
[[Category: Stadinski, B.D]]
[[Category: Blevins, S.J]]