7VTQ | pdb_00007vtq

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

PDB DOI: https://doi.org/10.2210/pdb7VTQ/pdb
EM Map EMD-32120: EMDB EMDataResource

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-10-30 Released: 2022-03-09
Deposition Author(s): Ohto, U., Shimizu, T.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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 1.2 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

PubMed: 35254907 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2121353119
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 1,466.95 kDa
Atom Count: 76,572
Modeled Residue Count: 9,468
Deposited Residue Count: 12,684
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	1,057	Mus musculus	Mutation(s): 0 Gene Names: NLRP3, NALP3 EC: 3.6.4
UniProt
Find proteins for Q8R4B8 (Mus musculus) Explore Q8R4B8 Go to UniProtKB: Q8R4B8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8R4B8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain GA [auth K] SDF format, chain M [auth A] SDF format, chain W [auth F] SDF format, chain Y [auth G] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain IA [auth L] SDF format, chain EA [auth J] SDF format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain GA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain IA [auth L] MOL2 format, chain EA [auth J] MOL2 format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain GA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain IA [auth L] mmCIF format, chain EA [auth J] mmCIF format, chain AA [auth H]	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		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
7YN (Subject of Investigation/LOI) Query on 7YN Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain HA [auth K] SDF format, chain V [auth E] SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth L] SDF format, chain FA [auth J] SDF format, chain DA [auth I] MOL2 format, chain BA [auth H] MOL2 format, chain HA [auth K] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth L] MOL2 format, chain FA [auth J] MOL2 format, chain DA [auth I] mmCIF format, chain BA [auth H] mmCIF format, chain HA [auth K] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth L] mmCIF format, chain FA [auth J] mmCIF format, chain DA [auth I]	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		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

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

Released Date: 2022-03-09

Deposition Author(s):

Ohto, U.

Shimizu, T.

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	20K16274
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	20K15730
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H00976