5irl - Revision history

OCA at 09:16, 20 March 2024

2024-03-20T09:16:57Z

←Older revision		Revision as of 09:16, 20 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/G1T469_RABIT G1T469_RABIT]		[https://www.uniprot.org/uniprot/G1T469_RABIT G1T469_RABIT]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a member of the NOD-like receptors family, are crucial for innate immune responses. Mutations of NOD2 have been associated with chronic inflammatory disorders such as Crohn's disease (CD), Blau syndrome (BS) and early-onset sarcoidosis (EOS), but little is known about its signalling mechanism and the role it plays in these diseases. Here, we report the crystal structure of rabbit NOD2 in an ADP-bound state. The structure reveals an inactive closed conformation in which the subdomains in the NOD domain are closely packed by ADP-mediated and inter-domain interactions. Mapping of the BS- or EOS-associated gain-of-function mutations reveals that most of these mutations are located in the NOD subdomain interfaces, and are likely to disrupt the inner domain interactions, facilitating a conformational change to the active form. Conversely, mutations associated with CD are distributed throughout the protein, some of which may affect oligomer formation and ligand binding.
-
-	Crystal structure of NOD2 and its implications in human disease.,Maekawa S, Ohto U, Shibata T, Miyake K, Shimizu T Nat Commun. 2016 Jun 10;7:11813. doi: 10.1038/ncomms11813. PMID:27283905<ref>PMID:27283905</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5irl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:07, 30 August 2023

2023-08-30T14:07:06Z

←Older revision		Revision as of 14:07, 30 August 2023
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	<StructureSection load='5irl' size='340' side='right'caption='[[5irl]], [[Resolution\|resolution]] 3.09Å' scene=''>		<StructureSection load='5irl' size='340' side='right'caption='[[5irl]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5irl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~European_rabbit European rabbit~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IRL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5irl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IRL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 3.09Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irm\|5irm]]~~, [[~~5irn~~\|~~5irn~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=9986 European rabbit])~~</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=5irl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irl OCA], [https://pdbe.org/5irl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5irl RCSB], [https://www.ebi.ac.uk/pdbsum/5irl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5irl 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=5irl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irl OCA], [~~http~~://pdbe.org/5irl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5irl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5irl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5irl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G1T469_RABIT G1T469_RABIT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: European rabbit]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Maekawa, S~~]]	+	[[Category: Oryctolagus cuniculus]]
-	[[Category: ~~Ohto, U~~]]	+	[[Category: Maekawa S]]
-	[[Category: ~~Shimizu, T~~]]	+	[[Category: Ohto U]]
-	[[Category: ~~Immune system]]~~	+	[[Category: Shimizu T]]
-	~~[[Category: Innate immunity]]~~	+
-	~~[[Category: Nod2~~]]	+

OCA at 07:17, 19 February 2020

2020-02-19T07:17:34Z

←Older revision		Revision as of 07:17, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state==		==Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state==
-	<StructureSection load='5irl' size='340' side='right' caption='[[5irl]], [[Resolution\|resolution]] 3.09Å' scene=''>	+	<StructureSection load='5irl' size='340' side='right'caption='[[5irl]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5irl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IRL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5irl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IRL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irm\|5irm]], [[5irn\|5irn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irm\|5irm]], [[5irn\|5irn]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NOD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9986 European rabbit])</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=5irl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irl OCA], [http://pdbe.org/5irl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5irl RCSB], [http://www.ebi.ac.uk/pdbsum/5irl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5irl 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=5irl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irl OCA], [http://pdbe.org/5irl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5irl RCSB], [http://www.ebi.ac.uk/pdbsum/5irl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5irl ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: European rabbit]]
		+	[[Category: Large Structures]]
	[[Category: Maekawa, S]]		[[Category: Maekawa, S]]
	[[Category: Ohto, U]]		[[Category: Ohto, U]]

OCA at 10:25, 13 July 2016

2016-07-13T10:25:36Z

←Older revision		Revision as of 10:25, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5irl is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state==
		+	<StructureSection load='5irl' size='340' side='right' caption='[[5irl]], [[Resolution\|resolution]] 3.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5irl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IRL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irm\|5irm]], [[5irn\|5irn]]</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=5irl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irl OCA], [http://pdbe.org/5irl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5irl RCSB], [http://www.ebi.ac.uk/pdbsum/5irl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5irl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a member of the NOD-like receptors family, are crucial for innate immune responses. Mutations of NOD2 have been associated with chronic inflammatory disorders such as Crohn's disease (CD), Blau syndrome (BS) and early-onset sarcoidosis (EOS), but little is known about its signalling mechanism and the role it plays in these diseases. Here, we report the crystal structure of rabbit NOD2 in an ADP-bound state. The structure reveals an inactive closed conformation in which the subdomains in the NOD domain are closely packed by ADP-mediated and inter-domain interactions. Mapping of the BS- or EOS-associated gain-of-function mutations reveals that most of these mutations are located in the NOD subdomain interfaces, and are likely to disrupt the inner domain interactions, facilitating a conformational change to the active form. Conversely, mutations associated with CD are distributed throughout the protein, some of which may affect oligomer formation and ligand binding.

-	~~Authors: Maekawa~~, S., Ohto, U., ~~Shimizu~~, T.	+	Crystal structure of NOD2 and its implications in human disease.,Maekawa S, Ohto U, Shibata T, Miyake K, Shimizu T Nat Commun. 2016 Jun 10;7:11813. doi: 10.1038/ncomms11813. PMID:27283905<ref>PMID:27283905</ref>

-	~~Description: Crystal structure~~ of ~~rabbit NOD2 SER mutant in an ADP-bound state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Shimizu, T]]~~	+	<div class="pdbe-citations 5irl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Maekawa, S]]		[[Category: Maekawa, S]]
	[[Category: Ohto, U]]		[[Category: Ohto, U]]
		+	[[Category: Shimizu, T]]
		+	[[Category: Immune system]]
		+	[[Category: Innate immunity]]
		+	[[Category: Nod2]]

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

2016-05-11T00:49:48Z

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

←Older revision

Revision as of 00:49, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5irl is ON HOLD until Paper Publication Authors: Maekawa, S., Ohto, U., Shimizu, T. Description: Crystal structure of rabbit NOD2 SER mutant in an ...

2016-05-11T00:49:47Z

New page: '''Unreleased structure''' The entry 5irl is ON HOLD until Paper Publication Authors: Maekawa, S., Ohto, U., Shimizu, T. Description: Crystal structure of rabbit NOD2 SER mutant in an ...

New page

'''Unreleased structure'''

The entry 5irl is ON HOLD until Paper Publication

Authors: Maekawa, S., Ohto, U., Shimizu, T.

Description: Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state
[[Category: Unreleased Structures]]
[[Category: Shimizu, T]]
[[Category: Maekawa, S]]
[[Category: Ohto, U]]