5y32 - Revision history

OCA at 08:20, 22 November 2023

OCA — Wed, 22 Nov 2023 08:20:44 GMT

←Older revision		Revision as of 08:20, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1==		==Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1==
-	<StructureSection load='5y32' size='340' side='right' caption='[[5y32]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5y32' size='340' side='right'caption='[[5y32]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y32]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yfc 4yfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y32 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y32 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y32]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yfc 4yfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y32 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=BMA:BETA-D-MANNOSE'~~>~~BMA</scene>, <scene name='pdbligand=FUC:ALPHA~~-~~L-FUCOSE'>FUC</scene>~~, ~~<scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.701Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Il1rapl1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10090 LK3 transgenic mice]), Ptprd ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Protein~~-~~tyrosine~~-~~phosphatase Protein~~-~~tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48]~~ </~~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=5y32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y32 OCA], [https://pdbe.org/5y32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y32 RCSB], [https://www.ebi.ac.uk/pdbsum/5y32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y32 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=5y32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y32 OCA], [~~http~~://pdbe.org/5y32 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y32 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y32 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y32 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IRPL1_MOUSE IRPL1_MOUSE]] May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel. May activate the MAP kinase JNK (By similarity). Plays a role in presynaptic and postsynaptic differentiation and dendritic spine formation in neurons.<ref>PMID:21940441</ref>	+	[https://www.uniprot.org/uniprot/IRPL1_MOUSE IRPL1_MOUSE] May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel. May activate the MAP kinase JNK (By similarity). Plays a role in presynaptic and postsynaptic differentiation and dendritic spine formation in neurons.<ref>PMID:21940441</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Tyrosine phosphatase\|Tyrosine phosphatase]]	+	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Protein-tyrosine-phosphatase~~]]	+	[[Category: Mus musculus]]
-	[[Category: Fukai, S]]	+	[[Category: Fukai S]]
-	[[Category: Yamagata, A]]	+	[[Category: Yamagata A]]
-	~~[[Category: Adhesion complex]]~~	+
-	~~[[Category: Immune system-hydrolase complex]]~~	+
-	~~[[Category: Trans-synaptic~~]]	+

OCA at 15:51, 27 February 2019

OCA — Wed, 27 Feb 2019 15:51:43 GMT

←Older revision		Revision as of 15:51, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='5y32' size='340' side='right' caption='[[5y32]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5y32' size='340' side='right' caption='[[5y32]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y32]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yfc 4yfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y32 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y32]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yfc 4yfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y32 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Il1rapl1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Ptprd ([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-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=5y32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y32 OCA], [http://pdbe.org/5y32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y32 RCSB], [http://www.ebi.ac.uk/pdbsum/5y32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y32 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=5y32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y32 OCA], [http://pdbe.org/5y32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y32 RCSB], [http://www.ebi.ac.uk/pdbsum/5y32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y32 ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/IRPL1_MOUSE IRPL1_MOUSE]] May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel. May activate the MAP kinase JNK (By similarity). Plays a role in presynaptic and postsynaptic differentiation and dendritic spine formation in neurons.<ref>PMID:21940441</ref>		[[http://www.uniprot.org/uniprot/IRPL1_MOUSE IRPL1_MOUSE]] May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel. May activate the MAP kinase JNK (By similarity). Plays a role in presynaptic and postsynaptic differentiation and dendritic spine formation in neurons.<ref>PMID:21940441</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Synapse formation is triggered through trans-synaptic interaction between pairs of pre- and postsynaptic adhesion molecules, the specificity of which depends on splice inserts known as 'splice-insert signaling codes'. Receptor protein tyrosine phosphatase delta (PTPdelta) can bidirectionally induce pre- and postsynaptic differentiation of neurons by trans-synaptically binding to interleukin-1 receptor accessory protein (IL-1RAcP) and IL-1RAcP-like-1 (IL1RAPL1) in a splicing-dependent manner. Here, we report crystal structures of PTPdelta in complex with IL1RAPL1 and IL-1RAcP. The first immunoglobulin-like (Ig) domain of IL1RAPL1 directly recognizes the first splice insert, which is critical for binding to IL1RAPL1. The second splice insert functions as an adjustable linker that positions the Ig2 and Ig3 domains of PTPdelta for simultaneously interacting with the Ig1 domain of IL1RAPL1 or IL-1RAcP. We further identified the IL1RAPL1-specific interaction, which appears coupled to the first-splice-insert-mediated interaction. Our results thus reveal the decoding mechanism of splice-insert signaling codes for synaptic differentiation induced by trans-synaptic adhesion between PTPdelta and IL1RAPL1/IL-1RAcP.
		+
		+	Mechanisms of splicing-dependent trans-synaptic adhesion by PTPdelta-IL1RAPL1/IL-1RAcP for synaptic differentiation.,Yamagata A, Yoshida T, Sato Y, Goto-Ito S, Uemura T, Maeda A, Shiroshima T, Iwasawa-Okamoto S, Mori H, Mishina M, Fukai S Nat Commun. 2015 Apr 24;6:6926. doi: 10.1038/ncomms7926. PMID:25908590<ref>PMID:25908590</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y32" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tyrosine phosphatase\|Tyrosine phosphatase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]

OCA: Protected "5y32" [edit=sysop:move=sysop]

OCA — Fri, 06 Oct 2017 05:35:45 GMT

Protected "5y32" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:35, 6 October 2017

OCA: New page: ==Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1== == Structural highlights ==
<table><tr><td colspan='2'>[[5y32]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4yfc 4yfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y32 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y32 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y32 OCA], [http://pdbe.org/5y32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y32 RCSB], [http://www.ebi.ac.uk/pdbsum/5y32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y32 ProSAT]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/IRPL1_MOUSE IRPL1_MOUSE]] May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel. May activate the MAP kinase JNK (By similarity). Plays a role in presynaptic and postsynaptic differentiation and dendritic spine formation in neurons.<ref>PMID:21940441</ref>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Protein-tyrosine-phosphatase]]
[[Category: Fukai, S]]
[[Category: Yamagata, A]]
[[Category: Adhesion complex]]
[[Category: Immune system-hydrolase complex]]
[[Category: Trans-synaptic]]