3QF2

Crystal structure of NALP3 PYD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal Structure of NALP3 Protein Pyrin Domain (PYD) and Its Implications in Inflammasome Assembly

Bae, J.Y., Park, H.H.

(2011) J.Biol.Chem. 286: 39528-39536

  • DOI: 10.1074/jbc.M111.278812

  • PubMed Abstract: 

    • NALP3 inflammasome, composed of the three proteins NALP3, ASC, and Caspase-1, is a macromolecular complex responsible for the innate immune response against infection with bacterial and viral pathogens. Formation of the inflammasome can lead to the a ...

    NALP3 inflammasome, composed of the three proteins NALP3, ASC, and Caspase-1, is a macromolecular complex responsible for the innate immune response against infection with bacterial and viral pathogens. Formation of the inflammasome can lead to the activation of inflammatory caspases, such as Caspase-1, which then activate pro-inflammatory cytokines by proteolytic cleavage. The assembly of the NALP3 inflammasome depends on the protein-interacting domain known as the death domain superfamily. NALP3 inflammasome is assembled via a pyrin domain (PYD)/PYD interaction between ASC and NALP3 and a caspase recruitment domain/caspase recruitment domain interaction between ASC and Caspase-1. As a first step toward elucidating the molecular mechanisms of inflammatory caspase activation by formation of inflammasome, we report the crystal structure of the PYD from NALP3 at 1.7-Å resolution. Although NALP3 PYD has the canonical six-helical bundle structural fold similar to other PYDs, the high resolution structure reveals the possible biologically important homodimeric interface and the dynamic properties of the fold. Comparison with other PYD structures shows both similarities and differences that may be functionally relevant. Structural and sequence analyses further implicate conserved surface residues in NALP3 PYD for ASC interaction and inflammasome assembly. The most interesting aspect of the structure was the unexpected disulfide bond between Cys-8 and Cys-108, which might be important for regulation of the activity of NALP3 by redox potential.

    Organizational Affiliation: 

    Graduate School of Biochemistry, and Research Institute of Protein Sensor, Yeungnam University, Gyeongsan, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NACHT, LRR and PYD domains-containing protein 3
A, B
110Homo sapiensMutation(s): 0 
Gene Names: NLRP3 (C1orf7, CIAS1, NALP3, PYPAF1)
Find proteins for Q96P20 (Homo sapiens)
Go to Gene View: NLRP3
Go to UniProtKB:  Q96P20
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.032α = 90.00
b = 60.040β = 107.62
c = 51.529γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
ADSCdata collection
SOLVEphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-01-21 
  • Released Date: 2011-08-31 
  • Deposition Author(s): Park, H.H., Bae, J.Y.

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Database references