6GFJ

Structure of RIP2 CARD domain fused to crystallisable MBP tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

RIP2 filament formation is required for NOD2 dependent NF-kappa B signalling.

Pellegrini, E.Desfosses, A.Wallmann, A.Schulze, W.M.Rehbein, K.Mas, P.Signor, L.Gaudon, S.Zenkeviciute, G.Hons, M.Malet, H.Gutsche, I.Sachse, C.Schoehn, G.Oschkinat, H.Cusack, S.

(2018) Nat Commun 9: 4043-4043

  • DOI: https://doi.org/10.1038/s41467-018-06451-3
  • Primary Citation of Related Structures:  
    6GFJ, 6GGS

  • PubMed Abstract: 

    Activation of the innate immune pattern recognition receptor NOD2 by the bacterial muramyl-dipeptide peptidoglycan fragment triggers recruitment of the downstream adaptor kinase RIP2, eventually leading to NF-κB activation and proinflammatory cytokine production. Here we show that full-length RIP2 can form long filaments mediated by its caspase recruitment domain (CARD), in common with other innate immune adaptor proteins. We further show that the NOD2 tandem CARDs bind to one end of the RIP2 CARD filament, suggesting a mechanism for polar filament nucleation by activated NOD2. We combine X-ray crystallography, solid-state NMR and high-resolution cryo-electron microscopy to determine the atomic structure of the helical RIP2 CARD filament, which reveals the intermolecular interactions that stabilize the assembly. Using structure-guided mutagenesis, we demonstrate the importance of RIP2 polymerization for the activation of NF-κB signalling by NOD2. Our results could be of use to develop new pharmacological strategies to treat inflammatory diseases characterised by aberrant NOD2 signalling.


  • Organizational Affiliation

    European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sugar ABC transporter substrate-binding protein,Receptor-interacting serine/threonine-protein kinase 2
A, B, C, D
477Methanosarcina mazeiHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEDU74_04045RIPK2CARDIAKRICKRIP2UNQ277/PRO314/PRO34092
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43353 (Homo sapiens)
Explore O43353 
Go to UniProtKB:  O43353
PHAROS:  O43353
GTEx:  ENSG00000104312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43353
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E, F, G, H
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.46α = 90
b = 121.57β = 109.04
c = 123.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary