4yh6 - Revision history

OCA at 08:14, 3 May 2023

OCA — Wed, 03 May 2023 08:14:04 GMT

←Older revision		Revision as of 08:14, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4yh6' size='340' side='right'caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4yh6' size='340' side='right'caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yh6]] is a 2 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=4YH6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yh6]] is a 2 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=4YH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YH6 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=MAN:ALPHA-D-MANNOSE'>MAN</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" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [https://pdbe.org/4yh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [https://www.ebi.ac.uk/pdbsum/4yh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh6 ProSAT]</span></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])</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [~~http~~://pdbe.org/4yh6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yh6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh6 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 25:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Fukai, S]]	+	[[Category: Fukai S]]
-	[[Category: Yamagata, A]]	+	[[Category: Yamagata A]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Synapse organizer~~]]	+

OCA at 06:52, 12 June 2019

OCA — Wed, 12 Jun 2019 06:52:22 GMT

←Older revision		Revision as of 06:52, 12 June 2019
Line 1:		Line 1:

	==Crystal structure of IL1RAPL1 ectodomain==		==Crystal structure of IL1RAPL1 ectodomain==
-	<StructureSection load='4yh6' size='340' side='right' caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='4yh6' size='340' side='right'caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yh6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yh6]] is a 2 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=4YH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YH6 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=MAN:ALPHA-D-MANNOSE'>MAN</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</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])</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [http://pdbe.org/4yh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh6 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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [http://pdbe.org/4yh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh6 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Yamagata, A]]		[[Category: Yamagata, A]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Synapse organizer]]		[[Category: Synapse organizer]]

OCA at 10:01, 10 March 2017

OCA — Fri, 10 Mar 2017 10:01:25 GMT

←Older revision		Revision as of 10:01, 10 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of IL1RAPL1 ectodomain==		==Crystal structure of IL1RAPL1 ectodomain==
	<StructureSection load='4yh6' size='340' side='right' caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='4yh6' size='340' side='right' caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 5:		Line 6:
	</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=MAN:ALPHA-D-MANNOSE'>MAN</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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh6 PDBsum]</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [http://pdbe.org/4yh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4yh6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:52, 6 May 2015

OCA — Wed, 06 May 2015 12:52:35 GMT

←Older revision		Revision as of 12:52, 6 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of IL1RAPL1 ectodomain==
		+	<StructureSection load='4yh6' size='340' side='right' caption='[[4yh6]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yh6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YH6 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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yh7\|4yh7]]</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=4yh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yh6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh6 PDBsum]</span></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>
		+	<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.

-	~~The entry 4yh6 is ON HOLD until Paper Publication~~	+	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>

-	~~Authors: Yamagata~~, A.~~, Fukai,~~ S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description:~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Yamagata, A]]		[[Category: Yamagata, A]]
		+	[[Category: Immune system]]
		+	[[Category: Synapse organizer]]

OCA at 12:25, 26 March 2015

OCA — Thu, 26 Mar 2015 12:25:58 GMT

←Older revision		Revision as of 12:25, 26 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yh6 is ON HOLD	+	The entry 4yh6 is ON HOLD until Paper Publication

	Authors: Yamagata, A., Fukai, S.		Authors: Yamagata, A., Fukai, S.

OCA: Protected "4yh6" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2015 10:29:07 GMT

Protected "4yh6" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:29, 4 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yh6 is ON HOLD Authors: Yamagata, A., Fukai, S. Description: Category: Unreleased Structures Category: Fukai, S Category: Yamagata, A

OCA — Wed, 04 Mar 2015 10:29:06 GMT

New page: '''Unreleased structure''' The entry 4yh6 is ON HOLD Authors: Yamagata, A., Fukai, S. Description: Category: Unreleased Structures Category: Fukai, S Category: Yamagata, A

New page

'''Unreleased structure'''

The entry 4yh6 is ON HOLD

Authors: Yamagata, A., Fukai, S.

Description:
[[Category: Unreleased Structures]]
[[Category: Fukai, S]]
[[Category: Yamagata, A]]