This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5irl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:16, 20 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='5irl' size='340' side='right'caption='[[5irl]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
<StructureSection load='5irl' size='340' side='right'caption='[[5irl]], [[Resolution|resolution]] 3.09&Aring;' 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]] 3.09&#8491;</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>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/G1T469_RABIT G1T469_RABIT]
-
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&reg;/PubMed&reg;, 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>
-
[[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]]
+

Current revision

Crystal structure of rabbit NOD2 SER mutant in an ADP-bound state

PDB ID 5irl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5irl"
Personal tools