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- PDB-5y3s: Crystal structure of human NLRP1 leucine rich repeat domain -

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Basic information

Entry
Database: PDB / ID: 5y3s
TitleCrystal structure of human NLRP1 leucine rich repeat domain
ComponentsNACHT, LRR and PYD domains-containing protein 1
KeywordsIMMUNE SYSTEM / inflammasome
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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / NACHT, LRR and PYD domains-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsJin, T. / Xiao, T.S.
CitationJournal: To Be Published
Title: Crystal structure of human NLRP1 LRR domain
Authors: Jin, T. / Xiao, T.S.
History
DepositionJul 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / reflns / Item: _citation.title / _reflns.pdbx_Rpim_I_all
Revision 1.2Nov 22, 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: NACHT, LRR and PYD domains-containing protein 1
B: NACHT, LRR and PYD domains-containing protein 1
C: NACHT, LRR and PYD domains-containing protein 1
D: NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3757
Polymers91,1624
Non-polymers2133
Water1448
1
A: NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9083
Polymers22,7901
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area9740 Å2
MethodPISA
2
B: NACHT, LRR and PYD domains-containing protein 1


Theoretical massNumber of molelcules
Total (without water)22,7901
Polymers22,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9710 Å2
MethodPISA
3
C: NACHT, LRR and PYD domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8852
Polymers22,7901
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-2 kcal/mol
Surface area9840 Å2
MethodPISA
4
D: NACHT, LRR and PYD domains-containing protein 1


Theoretical massNumber of molelcules
Total (without water)22,7901
Polymers22,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.480, 141.480, 294.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
NACHT, LRR and PYD domains-containing protein 1 / Caspase recruitment domain-containing protein 7 / Death effector filament-forming ced-4-like ...Caspase recruitment domain-containing protein 7 / Death effector filament-forming ced-4-like apoptosis protein / Nucleotide-binding domain and caspase recruitment domain


Mass: 22790.402 Da / Num. of mol.: 4 / Fragment: UNP residues 790-990
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 (E. coli) / References: UniProt: Q9C000
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.6M Sodium Potassium Phosphate, 100mM HEPES, pH 6.4

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.451→33.76 Å / Num. obs: 41422 / % possible obs: 98.9 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0572 / Rpim(I) all: 0.0268 / Net I/σ(I): 18.99
Reflection shellResolution: 2.451→2.539 Å / Rmerge(I) obs: 0.9533 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFJ

1dfj


Resolution: 2.451→33.76 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.82
RfactorNum. reflection% reflection
Rfree0.2588 2061 4.98 %
Rwork0.2115 --
obs0.2139 41416 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.451→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 11 8 6207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096282
X-RAY DIFFRACTIONf_angle_d1.0698480
X-RAY DIFFRACTIONf_dihedral_angle_d10.115122
X-RAY DIFFRACTIONf_chiral_restr0.0491028
X-RAY DIFFRACTIONf_plane_restr0.0051092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4511-2.50810.32131460.29942579X-RAY DIFFRACTION99
2.5081-2.57080.33321510.28962595X-RAY DIFFRACTION100
2.5708-2.64030.36711360.29022597X-RAY DIFFRACTION100
2.6403-2.7180.31451490.27212628X-RAY DIFFRACTION100
2.718-2.80570.30541310.25232604X-RAY DIFFRACTION100
2.8057-2.9060.29981430.24882624X-RAY DIFFRACTION100
2.906-3.02230.33941390.25812634X-RAY DIFFRACTION100
3.0223-3.15980.30731340.26782609X-RAY DIFFRACTION100
3.1598-3.32640.30871290.25842630X-RAY DIFFRACTION99
3.3264-3.53470.29321320.22892649X-RAY DIFFRACTION99
3.5347-3.80750.2681290.20412618X-RAY DIFFRACTION99
3.8075-4.19050.23351460.18822601X-RAY DIFFRACTION98
4.1905-4.79630.2081310.17212629X-RAY DIFFRACTION98
4.7963-6.04080.25071410.20632647X-RAY DIFFRACTION98
6.0408-47.06790.20821240.17552711X-RAY DIFFRACTION96

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