7BSO

Crystal structure of the human NLRP9 pyrin domain

• PDB DOI: https://doi.org/10.2210/pdb7BSO/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-03-31 Released: 2021-02-10 
• Deposition Author(s): Park, H.H., Ha, H.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.282 
• R-Value Work: 0.213 

Literature

Crystal structure of the human NLRP9 pyrin domain reveals a bent N-terminal loop that may regulate inflammasome assembly.

Ha, H.J., Park, H.H.

(2020) FEBS Lett 594: 2396-2405

• PubMed: 32542766 
• DOI: https://doi.org/10.1002/1873-3468.13866
• Primary Citation of Related Structures:  
  7BSO


• PubMed Abstract: 
  

  Members of the NLR family pyrin domain containing (NLRPs) are pattern recognition receptors that participate in innate immunity. They form inflammasomes, which are platforms for caspase-1 recruitment and activation. The NLRP pyrin domain (PYD) is critical for the assembly of inflammasomes due to its ability to mediate protein interactions. Despite intensive structural studies on inflammasomes with PYDs, the structure of the PYD of NLRP9-the least studied member of the family-remains unknown. Herein, we report the crystal structure of the human NLRP9 PYD at 2.1 Å resolution, which reveals a kinked N-terminal loop oriented toward the interior of the helical bundle. Based on our findings, we propose a regulatory role for the kinked N-terminal loop of NLRP9 PYD in inflammasome assembly.

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Organizational Affiliation: 

College of Pharmacy, Chung-Ang University, Seoul, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 12.81 kDa 
• Atom Count: 800 
• Modelled Residue Count: 90 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 9	A	104	Homo sapiens	Mutation(s): 0  Gene Names: NLRP9, NALP9
UniProt & NIH Common Fund Data Resources
Find proteins for Q7RTR0 (Homo sapiens) Explore Q7RTR0  Go to UniProtKB:  Q7RTR0
PHAROS:  Q7RTR0 GTEx:  ENSG00000185792

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.282 
• R-Value Work: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.97	α = 90
b = 33.685	β = 102.397
c = 49.667	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Park, H.H., Ha, H.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description