6Z2G

Crystal structure of human NLRP9 PYD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly.

Marleaux, M.Anand, K.Latz, E.Geyer, M.

(2020) FEBS Lett 594: 2383-2395

  • DOI: https://doi.org/10.1002/1873-3468.13865
  • Primary Citation of Related Structures:  
    6Z2G

  • PubMed Abstract: 

    Inflammasomes are cytosolic multimeric signaling complexes of the innate immune system that induce activation of caspases. The NOD-like receptor NLRP9 recruits the adaptor protein ASC to form an ASC-dependent inflammasome to limit rotaviral replication in intestinal epithelial cells, but only little is known about the molecular mechanisms regulating and driving its assembly. Here, we present the crystal structure of the human NLRP9 pyrin domain (PYD). We show that NLRP9 PYD is not able to self-polymerize nor to nucleate ASC specks in HEK293T cells. A comparison with filament-forming PYDs revealed that NLRP9 PYD adopts a conformation compatible with filament formation, but several charge inversions of interfacing residues might cause repulsive effects that prohibit self-oligomerization. These results propose that inflammasome assembly of NLRP9 might differ largely from what we know of other inflammasomes.


  • Organizational Affiliation

    Institute of Structural Biology, University of Bonn, Bonn, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 999Homo sapiensMutation(s): 0 
Gene Names: NLRP9NALP9NOD6PAN12
UniProt & NIH Common Fund Data Resources
Find proteins for Q7RTR0 (Homo sapiens)
Explore Q7RTR0 
Go to UniProtKB:  Q7RTR0
PHAROS:  Q7RTR0
GTEx:  ENSG00000185792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7RTR0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.33α = 90
b = 33.33β = 90
c = 311.091γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany2014_A203

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description