7ALV

Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition.

Dekker, C.Mattes, H.Wright, M.Boettcher, A.Hinniger, A.Hughes, N.Kapps-Fouthier, S.Eder, J.Erbel, P.Stiefl, N.Mackay, A.Farady, C.J.

(2021) J Mol Biol 433: 167309-167309

  • DOI: 10.1016/j.jmb.2021.167309
  • Primary Citation of Related Structures:  
    7ALV

  • PubMed Abstract: 
  • The NLRP3 inflammasome assembles in response to a variety of pathogenic and sterile danger signals, resulting in the production of interleukin-1β and interleukin-18. NLRP3 is a key component of the innate immune system and has been implicated as a driver of a number of acute and chronic diseases ...

    The NLRP3 inflammasome assembles in response to a variety of pathogenic and sterile danger signals, resulting in the production of interleukin-1β and interleukin-18. NLRP3 is a key component of the innate immune system and has been implicated as a driver of a number of acute and chronic diseases. We report the 2.8 Å crystal structure of the NLRP3 NACHT domain in complex with an inhibitor. The structure defines a binding pocket formed by the four subdomains of the NACHT domain, and shows the inhibitor acts as an intramolecular glue, which locks the protein in an inactive conformation. It provides further molecular insight into our understanding of NLRP3 activation, helps to detail the residues involved in subdomain coordination within the NLRP3 NACHT domain, and gives molecular insights into how gain-of-function mutations de-stabilize the inactive conformation of NLRP3. Finally, it suggests stabilizing the auto-inhibited form of the NACHT domain is an effective way to inhibit NLRP3, and will aid the structure-based development of NLRP3 inhibitors for a range of inflammatory diseases.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, CH-4056 Basel, Switzerland. Electronic address: christopher.farady@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 3A550Homo sapiensMutation(s): 0 
Gene Names: NLRP3C1orf7CIAS1NALP3PYPAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P20 (Homo sapiens)
Explore Q96P20 
Go to UniProtKB:  Q96P20
PHAROS:  Q96P20
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RM5
Query on RM5

Download Ideal Coordinates CCD File 
B [auth A]1-[4-chloranyl-2,6-di(propan-2-yl)phenyl]-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea
C20 H27 Cl N2 O5 S
RTJGVFANTDWUEG-UHFFFAOYSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.18α = 90
b = 96.18β = 90
c = 262.54γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
STARANISOdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-17
    Changes: Data collection, Database references