+Open data
-Basic information
Entry | Database: PDB / ID: 7crv | ||||||
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Title | Crystal structure of rNLRP1-FIIND | ||||||
Components | (NLR family protein 1) x 2 | ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / programmed necrotic cell death / positive regulation of pyroptotic inflammatory response / self proteolysis / stress-activated protein kinase signaling cascade / Hydrolases; Acting on peptide bonds (peptidases) ...negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / programmed necrotic cell death / positive regulation of pyroptotic inflammatory response / self proteolysis / stress-activated protein kinase signaling cascade / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor activity / cellular response to UV-B / pyroptotic inflammatory response / response to muramyl dipeptide / antiviral innate immune response / signaling adaptor activity / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / protein homooligomerization / positive regulation of inflammatory response / : / double-stranded RNA binding / peptidase activity / scaffold protein binding / double-stranded DNA binding / regulation of apoptotic process / neuron apoptotic process / defense response to virus / defense response to bacterium / protein domain specific binding / neuronal cell body / enzyme binding / ATP hydrolysis activity / protein-containing complex / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Huang, M.H. / Zhang, X.X. / Wang, J. / Chai, J.J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2021 Title: Structural and biochemical mechanisms of NLRP1 inhibition by DPP9. Authors: Menghang Huang / Xiaoxiao Zhang / Gee Ann Toh / Qin Gong / Jia Wang / Zhifu Han / Bin Wu / Franklin Zhong / Jijie Chai / Abstract: Nucleotide-binding domain, leucine-rich repeat receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires autocleavage within its function-to-find ...Nucleotide-binding domain, leucine-rich repeat receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires autocleavage within its function-to-find domain (FIIND). In resting cells, the dipeptidyl peptidases DPP8 and DPP9 interact with the FIIND of NLRP1 and suppress spontaneous NLRP1 activation; however, the mechanisms through which this occurs remain unknown. Here we present structural and biochemical evidence that full-length rat NLRP1 (rNLRP1) and rat DPP9 (rDPP9) form a 2:1 complex that contains an autoinhibited rNLRP1 molecule and an active UPA-CARD fragment of rNLRP1. The ZU5 domain is required not only for autoinhibition of rNLRP1 but also for assembly of the 2:1 complex. Formation of the complex prevents UPA-mediated higher-order oligomerization of UPA-CARD fragments and strengthens ZU5-mediated NLRP1 autoinhibition. Structure-guided biochemical and functional assays show that both NLRP1 binding and enzymatic activity are required for DPP9 to suppress NLRP1 in human cells. Together, our data reveal the mechanism of DPP9-mediated inhibition of NLRP1 and shed light on the activation of the NLRP1 inflammasome. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7crv.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7crv.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 7crv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7crv_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
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Full document | 7crv_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 7crv_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7crv_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/7crv ftp://data.pdbj.org/pub/pdb/validation_reports/cr/7crv | HTTPS FTP |
-Related structure data
Related structure data | 7crwC 3g5bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20764.316 Da / Num. of mol.: 2 / Fragment: ZU5 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nlrp1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9I2G3 #2: Protein | Mass: 17649.637 Da / Num. of mol.: 2 / Fragment: UPA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nlrp1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D9I2G3 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.0M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 1% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 43870 / % possible obs: 99.9 % / Redundancy: 19.3 % / Biso Wilson estimate: 31.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 4107 / CC1/2: 0.776 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G5B Resolution: 2→28.76 Å / SU ML: 0.2651 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6481 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.76 Å
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Refine LS restraints |
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LS refinement shell |
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