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- PDB-8zgd: The Crystal Structure of the NLRP1_LRR domain from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8zgd
TitleThe Crystal Structure of the NLRP1_LRR domain from Biortus.
ComponentsNACHT, LRR and PYD domains-containing protein 1, N-terminus
KeywordsSTRUCTURAL PROTEIN / Hydrolase / Protease
Function / homology
Function and homology information


NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B ...NLRP1 inflammasome complex assembly / cysteine-type endopeptidase activator activity / NLRP1 inflammasome complex / canonical inflammasome complex / The NLRP1 inflammasome / self proteolysis / Hydrolases; Acting on peptide bonds (peptidases) / pattern recognition receptor signaling pathway / pattern recognition receptor activity / cellular response to UV-B / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / response to muramyl dipeptide / antiviral innate immune response / signaling adaptor 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 / defense response to bacterium / protein domain specific binding / apoptotic process / nucleolus / enzyme binding / signal transduction / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
FIIND domain / Function to find / 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 / DAPIN domain / DAPIN domain profile. ...FIIND domain / Function to find / 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 / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine Rich Repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine-rich repeat profile. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of the NLRP1_LRR domain from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Pan, W.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 1, N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4252
Polymers22,3331
Non-polymers921
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-2 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.582, 84.582, 132.495
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1161-

HOH

21A-1264-

HOH

31A-1265-

HOH

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 1, N-terminus / NLRP1-NT


Mass: 22332.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9C000
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20mM MgCl2, 0.1M Tris pH 8.0, 19% polyacrylic acid 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.952989 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.952989 Å / Relative weight: 1
ReflectionResolution: 2.05→49.13 Å / Num. obs: 18288 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 13.5
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.964 / Num. unique obs: 1387

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.13 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.428 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.152 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2209 916 5.023 %
Rwork0.1757 17320 -
all0.178 --
obs-18236 99.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.717 Å2
Baniso -1Baniso -2Baniso -3
1--0.173 Å2-0.087 Å2-0 Å2
2---0.173 Å20 Å2
3---0.562 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 6 188 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161600
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.8632156
X-RAY DIFFRACTIONr_angle_other_deg0.6541.7813688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.628518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0210315
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.51070
X-RAY DIFFRACTIONr_chiral_restr0.0970.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined0.2390.2355
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21479
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2930
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2148
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1890.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0890.210
X-RAY DIFFRACTIONr_nbd_other0.1340.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2720.213
X-RAY DIFFRACTIONr_mcbond_it2.6962.053799
X-RAY DIFFRACTIONr_mcbond_other2.6852.052799
X-RAY DIFFRACTIONr_mcangle_it4.0123.6731000
X-RAY DIFFRACTIONr_mcangle_other4.0123.6831001
X-RAY DIFFRACTIONr_scbond_it4.1342.743796
X-RAY DIFFRACTIONr_scbond_other4.1312.743797
X-RAY DIFFRACTIONr_scangle_it6.7614.7411150
X-RAY DIFFRACTIONr_scangle_other6.7584.7411151
X-RAY DIFFRACTIONr_lrange_it9.23221.911851
X-RAY DIFFRACTIONr_lrange_other9.1621.3841806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.231680.2231248X-RAY DIFFRACTION99.9241
2.103-2.1610.225630.2121217X-RAY DIFFRACTION100
2.161-2.2230.217670.1891183X-RAY DIFFRACTION100
2.223-2.2910.241690.1761137X-RAY DIFFRACTION99.9172
2.291-2.3660.294580.1771113X-RAY DIFFRACTION100
2.366-2.4490.209620.1721070X-RAY DIFFRACTION100
2.449-2.5420.213490.1661064X-RAY DIFFRACTION100
2.542-2.6450.212430.1861024X-RAY DIFFRACTION100
2.645-2.7620.221490.174971X-RAY DIFFRACTION100
2.762-2.8970.255510.182936X-RAY DIFFRACTION100
2.897-3.0530.279460.193898X-RAY DIFFRACTION100
3.053-3.2370.255420.186848X-RAY DIFFRACTION100
3.237-3.460.204460.171792X-RAY DIFFRACTION100
3.46-3.7350.18330.146764X-RAY DIFFRACTION100
3.735-4.0890.178400.142690X-RAY DIFFRACTION100
4.089-4.5680.188300.137647X-RAY DIFFRACTION100
4.568-5.2670.196290.165576X-RAY DIFFRACTION100
5.267-6.4330.258360.219480X-RAY DIFFRACTION99.422
6.433-9.020.277180.2404X-RAY DIFFRACTION100
9.02-49.130.168170.193258X-RAY DIFFRACTION100

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