7WBT | pdb_00007wbt

Crystal structure of bovine NLRP9

• PDB DOI: https://doi.org/10.2210/pdb7WBT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-12-17 Released: 2022-04-06 
• Deposition Author(s): Kamitsukasa, Y., Shimizu, T., Ohto, U.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

The structure of NLRP9 reveals a unique C-terminal region with putative regulatory function.

Kamitsukasa, Y., Nakano, K., Murakami, K., Hirata, K., Yamamoto, M., Shimizu, T., Ohto, U.

(2022) FEBS Lett 596: 876-885

• PubMed: 35090055 
• DOI: https://doi.org/10.1002/1873-3468.14302
• Primary Citation of Related Structures:  
  7WBT, 7WBU


• PubMed Abstract: 
  

  Nucleotide-binding and oligomerisation domain-like receptors (NLRs) can form inflammasomes that activate caspase-1 and pro-interleukin-1β and induce pyroptosis. NLR family pyrin domain-containing 9 (NLRP9) forms an inflammasome and activates innate immune responses during virus infection, but little is known about this process. Here, we report the crystal and cryo-electron microscopy structures of NLRP9 in an ADP-bound state, revealing inactive and closed conformations of NLRP9 and its similarities to other structurally characterised NLRs. Moreover, we found a C-terminal region interacting with the concave surface of the leucine-rich repeat domain of NLRP9. This region is unique among NLRs and might be involved in the specific function of NLRP9. These data provide the structural basis for understanding the mechanism of NLRP9 regulation and activation.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
RIKEN SPring-8 Center, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 209 kDa 
• Atom Count: 14,366 
• Modeled Residue Count: 1,798 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 9	A, B	912	Bos taurus	Mutation(s): 0  Gene Names: NLRP9, NALP9
UniProt
Find proteins for Q288C4 (Bos taurus) Explore Q288C4  Go to UniProtKB:  Q288C4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.26	α = 90
b = 169.12	β = 90
c = 177.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Kamitsukasa, Y., Shimizu, T., Ohto, U.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H03164
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H00976

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-04-27
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary