5IRM image
Deposition Date 2016-03-14
Release Date 2016-06-29
Last Version Date 2024-03-20
Entry Detail
PDB ID:
5IRM
Keywords:
Title:
Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form2)
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.31 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):NOD2
Chain IDs:A, B (auth: C)
Chain Length:830
Number of Molecules:2
Biological Source:Oryctolagus cuniculus
Ligand Molecules
Primary Citation
Crystal structure of NOD2 and its implications in human disease.
Nat Commun 7 11813 11813 (2016)
PMID: 27283905 DOI: 10.1038/ncomms11813

Abstact

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.

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Disease

Primary Citation of related structures