5IRL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of NOD2 and its implications in human disease.

Maekawa, S.Ohto, U.Shibata, T.Miyake, K.Shimizu, T.

(2016) Nat Commun 7: 11813-11813

  • DOI: https://doi.org/10.1038/ncomms11813
  • Primary Citation of Related Structures:  
    5IRL, 5IRM, 5IRN

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein830Oryctolagus cuniculusMutation(s): 2 
Gene Names: NOD2
UniProt
Find proteins for G1T469 (Oryctolagus cuniculus)
Explore G1T469 
Go to UniProtKB:  G1T469
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1T469
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.9α = 90
b = 107.845β = 90
c = 185.365γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references