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- PDB-7crv: Crystal structure of rNLRP1-FIIND -

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Basic information

Entry
Database: PDB / ID: 7crv
TitleCrystal structure of rNLRP1-FIIND
Components(NLR family protein 1) x 2
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / programmed necrotic cell death / NLRP3 inflammasome complex / self proteolysis / positive regulation of pyroptotic inflammatory response / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to UV-B ...negative regulation of cellular defense response / NLRP1 inflammasome complex assembly / NLRP1 inflammasome complex / programmed necrotic cell death / NLRP3 inflammasome complex / self proteolysis / positive regulation of pyroptotic inflammatory response / cysteine-type endopeptidase activator activity / Hydrolases; Acting on peptide bonds (peptidases) / cellular response to UV-B / pattern recognition receptor activity / pyroptotic inflammatory response / response to muramyl dipeptide / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / intrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / protein homooligomerization / positive regulation of inflammatory response / peptidase activity / double-stranded RNA binding / double-stranded DNA binding / regulation of inflammatory response / scaffold protein binding / neuron apoptotic process / regulation of apoptotic process / defense response to virus / defense response to bacterium / inflammatory response / protein domain specific binding / neuronal cell body / enzyme binding / signal transduction / protein-containing complex / ATP hydrolysis activity / ATP binding / nucleus / cytosol
Similarity search - Function
FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain ...FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / CARD8/ASC/NALP1, CARD domain / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 1 allele 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, M.H. / Zhang, X.X. / Wang, J. / Chai, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31421001 to J.C. China
CitationJournal: 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
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_detector / diffrn_source
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NLR family protein 1
D: NLR family protein 1
C: NLR family protein 1
B: NLR family protein 1


Theoretical massNumber of molelcules
Total (without water)76,8284
Polymers76,8284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-81 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.955, 83.955, 156.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein NLR family protein 1


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 NLR family protein 1


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2→2.03 Å / Num. unique obs: 4107 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.18.2-3874model building
PHENIX1.18.2-3874phasing
PHENIX1.18.2-3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G5B

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
RfactorNum. reflection% reflection
Rfree0.2593 2194 5.01 %
Rwork0.2245 41589 -
obs0.2263 43783 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.34 Å2
Refinement stepCycle: LAST / Resolution: 2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 0 4542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064671
X-RAY DIFFRACTIONf_angle_d1.38576361
X-RAY DIFFRACTIONf_chiral_restr0.1624711
X-RAY DIFFRACTIONf_plane_restr0.0097816
X-RAY DIFFRACTIONf_dihedral_angle_d15.8279616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.35581170.29342550X-RAY DIFFRACTION98.92
2.04-2.090.34851470.28922560X-RAY DIFFRACTION100
2.09-2.140.36851200.27822563X-RAY DIFFRACTION100
2.14-2.20.34371190.26612577X-RAY DIFFRACTION100
2.2-2.270.3371590.27962556X-RAY DIFFRACTION99.96
2.27-2.340.33281240.27172588X-RAY DIFFRACTION100
2.34-2.420.29731330.27162552X-RAY DIFFRACTION100
2.42-2.520.30431490.26822589X-RAY DIFFRACTION100
2.52-2.640.30851360.27682579X-RAY DIFFRACTION100
2.64-2.770.30661040.27882627X-RAY DIFFRACTION100
2.77-2.950.32951370.26812576X-RAY DIFFRACTION100
2.95-3.170.32381350.25092618X-RAY DIFFRACTION100
3.18-3.490.23991220.22352650X-RAY DIFFRACTION100
3.49-40.25051880.19452574X-RAY DIFFRACTION100
4-5.030.16141540.16172649X-RAY DIFFRACTION100
5.04-28.760.21841500.17732781X-RAY DIFFRACTION99.63

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