+Open data
-Basic information
Entry | Database: PDB / ID: 6x6c | ||||||
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Title | Cryo-EM structure of NLRP1-DPP9-VbP complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / NLRP1 / DPP9 / inflammasome / Val-boroPro (VbP) / talabostat / innate immunity | ||||||
Function / homology | Function and homology information NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / dipeptidyl-peptidase IV / self proteolysis / dipeptidyl-peptidase activity / negative regulation of programmed cell death / Hydrolases; Acting on peptide bonds (peptidases) ...NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / dipeptidyl-peptidase IV / self proteolysis / dipeptidyl-peptidase activity / negative regulation of programmed cell death / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B / cell leading edge / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / response to muramyl dipeptide / antiviral innate immune response / aminopeptidase activity / signaling adaptor activity / serine-type peptidase activity / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / : / double-stranded RNA binding / peptidase activity / regulation of inflammatory response / double-stranded DNA binding / regulation of apoptotic process / neuron apoptotic process / defense response to virus / microtubule / defense response to bacterium / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / proteolysis / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
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. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2021 Title: DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation. Authors: L Robert Hollingsworth / Humayun Sharif / Andrew R Griswold / Pietro Fontana / Julian Mintseris / Kevin B Dagbay / Joao A Paulo / Steven P Gygi / Daniel A Bachovchin / Hao Wu / 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 ...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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6x6c.cif.gz | 402 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x6c.ent.gz | 304.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x6c_validation.pdf.gz | 858.3 KB | Display | wwPDB validaton report |
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Full document | 6x6c_full_validation.pdf.gz | 880.3 KB | Display | |
Data in XML | 6x6c_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 6x6c_validation.cif.gz | 94.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/6x6c ftp://data.pdbj.org/pub/pdb/validation_reports/x6/6x6c | HTTPS FTP |
-Related structure data
Related structure data | 22075MC 6x6aC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10595 (Title: Human NLRP1-DPP9-VbP complex / Data size: 1.2 TB Data #1: Unaligned multi frame micographs of NLRP1-DPP9-VbP-noTILT [micrographs - focal pairs - unprocessed] Data #2: Unaligned multi frame micographs of NLRP1-DPP9-VbP-TILT [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 101761.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV #2: Protein | Mass: 166069.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9C000 #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DPP9-NLRP1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pcDNA3.1 |
Buffer solution | pH: 7.5 / Details: 25 mM Tris pH 7.5, 150 mM NaCl, 1 mM TCEP |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | |||||||||||||||
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN | |||||||||||||||
Electron lens | Mode: OTHER / Calibrated magnification: 10500 X / Nominal defocus max: 2200 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm | |||||||||||||||
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | |||||||||||||||
Image recording | Imaging-ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4
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-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205538 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
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