6NPY

Cryo-EM structure of NLRP3 bound to NEK7


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.

Sharif, H.Wang, L.Wang, W.L.Magupalli, V.G.Andreeva, L.Qiao, Q.Hauenstein, A.V.Wu, Z.Nunez, G.Mao, Y.Wu, H.

(2019) Nature 570: 338-343

  • DOI: https://doi.org/10.1038/s41586-019-1295-z
  • Primary Citation of Related Structures:  
    6NPY

  • PubMed Abstract: 

    The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 31,034Homo sapiensMutation(s): 4 
Gene Names: NLRP3C1orf7CIAS1NALP3PYPAF1
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P20 (Homo sapiens)
Explore Q96P20 
Go to UniProtKB:  Q96P20
PHAROS:  Q96P20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96P20
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase R,Serine/threonine-protein kinase Nek7279Homo sapiensMutation(s): 8 
Gene Names: EIF2AK2PKRPRKRNEK7
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.34 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDX7 (Homo sapiens)
Explore Q8TDX7 
Go to UniProtKB:  Q8TDX7
PHAROS:  Q8TDX7
GTEx:  ENSG00000151414 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1R01 Al124491
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States1DP1 HD087988

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references
  • Version 2.0: 2019-08-14
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.2: 2024-03-20
    Changes: Data collection, Database references