6X6C

Cryo-EM structure of NLRP1-DPP9-VbP complex

Summary for 6X6C

• Entry DOI: 10.2210/pdb6x6c/pdb
• EMDB information: 22075
• Descriptor: Dipeptidyl peptidase 9, NACHT, LRR and PYD domains-containing protein 1, [(2~{R})-1-[(2~{R})-2-azanyl-3-methyl-butanoyl]pyrrolidin-2-yl]boronic acid (3 entities in total)
• Functional Keywords: nlrp1, dpp9, inflammasome, val-boropro (vbp), talabostat, innate immunity, immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 536091.08

Authors

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. (deposition date: 2020-05-27, release date: 2021-03-10, Last modification date: 2021-05-12)

Primary citation

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.
DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation.
Nature, 592:778-783, 2021

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. Gain-of-function mutations of NLRP1 cause severe inflammatory diseases of the skin. NLRP1 contains a function-to-find domain that auto-proteolyses into noncovalently associated subdomains, and proteasomal degradation of the repressive N-terminal fragment of NLRP1 releases its inflammatory C-terminal fragment (NLRP1 CT). 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. 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 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.

PubMed: 33731932
DOI: 10.1038/s41586-021-03350-4

Experimental method

ELECTRON MICROSCOPY (2.9 Å)