6X6C

Cryo-EM structure of NLRP1-DPP9-VbP complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation.

Hollingsworth, L.R.Sharif, H.Griswold, A.R.Fontana, P.Mintseris, J.Dagbay, K.B.Paulo, J.A.Gygi, S.P.Bachovchin, D.A.Wu, H.

(2021) Nature 592: 778-783

  • DOI: 10.1038/s41586-021-03350-4
  • Primary Citation of Related Structures:  
    6X6A, 6X6C

  • PubMed Abstract: 
  • Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 1 (NLRP1) is an inflammasome sensor that mediates the activation of caspase-1 to induce cytokine maturation and pyroptosis 1-4 . Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin 4-6 ...

    Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 1 (NLRP1) is an inflammasome sensor that mediates the activation of caspase-1 to induce cytokine maturation and pyroptosis 1-4 . Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin 4-6 . NLRP1 contains a function-to-find domain that auto-proteolyses into noncovalently associated subdomains 7-9 , and proteasomal degradation of the repressive N-terminal fragment of NLRP1 releases its inflammatory C-terminal fragment (NLRP1 CT) 10,11 . Cytosolic dipeptidyl peptidases 8 and 9 (hereafter, DPP8/DPP9) both interact with NLRP1, and small-molecule inhibitors of DPP8/DPP9 activate NLRP1 by mechanisms that are currently unclear 10,12-14 . Here we report cryo-electron microscopy structures of the human NLRP1-DPP9 complex alone and with Val-boroPro (VbP), an inhibitor of DPP8/DPP9. The structures reveal a ternary complex that comprises DPP9, full-length NLRP1 and the NLRPT CT. The binding of the NLRP1 CT to DPP9 requires full-length NLRP1, which suggests that NLRP1 activation is regulated by the ratio of NLRP1 CT to full-length NLRP1. Activation of the inflammasome by ectopic expression of the NLRP1 CT is consistently rescued by co-expression of autoproteolysis-deficient full-length NLRP1. The N terminus of the NLRP1 CT inserts into the DPP9 active site, and VbP disrupts this interaction. Thus, VbP weakens the NLRP1-DPP9 interaction and accelerates degradation of the N-terminal fragment 10 to induce inflammasome activation. Overall, these data demonstrate that DPP9 quenches low levels of NLRP1 CT and thus serves as a checkpoint for activation of the NLRP1 inflammasome.


    Organizational Affiliation

    Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. wu@crystal.harvard.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 9A, B [auth D]891Homo sapiensMutation(s): 0 
Gene Names: DPP9DPRP2
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TI2 (Homo sapiens)
Explore Q86TI2 
Go to UniProtKB:  Q86TI2
PHAROS:  Q86TI2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 1C [auth E], D [auth F]1473Homo sapiensMutation(s): 0 
Gene Names: NLRP1CARD7DEFCAPKIAA0926NACNALP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C000 (Homo sapiens)
Explore Q9C000 
Go to UniProtKB:  Q9C000
PHAROS:  Q9C000
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GK2 (Subject of Investigation/LOI)
Query on GK2

Download Ideal Coordinates CCD File 
E [auth A], F [auth D][(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid
C9 H19 B N2 O3
FKCMADOPPWWGNZ-JGVFFNPUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 Al124491

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references, Structure summary
  • Version 1.2: 2021-05-12
    Changes: Database references