7VTQ

Cryo-EM structure of mouse NLRP3 (full-length) dodecamer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


Literature

Structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation.

Ohto, U., Kamitsukasa, Y., Ishida, H., Zhang, Z., Murakami, K., Hirama, C., Maekawa, S., Shimizu, T.

(2022) Proc Natl Acad Sci U S A 119: e2121353119-e2121353119

  • DOI: https://doi.org/10.1073/pnas.2121353119
  • Primary Citation of Related Structures:  
    7VTP, 7VTQ

  • PubMed Abstract: 

    SignificanceThe nucleotide-binding oligomerization domain (NOD)-like receptor pyrin domain containing 3 (NLRP3) is a pattern recognition receptor that forms an inflammasome. The cryo-electron microscopy structure of the dodecameric form of full-length NLRP3 bound to the clinically relevant NLRP3-specific inhibitor MCC950 has established the structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation and the mechanism of action of the NLRP3 specific inhibitor. The inactive NLRP3 oligomer represents the NLRP3 resting state, capable of binding to membranes and is likely disrupted for its activation. Visualization of the inhibitor binding mode will enable optimization of the activity of NLRP3 inflammasome inhibitor drugs.

    • Organizational Affiliation: 

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 3
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
1,057Mus musculusMutation(s): 0 
Gene Names: NLRP3, NALP3
UniProt
Find proteins for Q8R4B8 (Mus musculus)
Explore Q8R4B8 
Go to UniProtKB:  Q8R4B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R4B8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
IA [auth L]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
IA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
7YN (Subject of Investigation/LOI)
Query on 7YN
Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea
C20 H22 N2 O5 S
WBBMLFLTCGFUSC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H03164
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan20K16274
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan20K15730
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H00976

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references