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- PDB-7bso: Crystal structure of the human NLRP9 pyrin domain -

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Basic information

Entry
Database: PDB / ID: 7bso
TitleCrystal structure of the human NLRP9 pyrin domain
ComponentsNACHT, LRR and PYD domains-containing protein 9
KeywordsAPOPTOSIS / sensor component / NLRP9 inflammasome
Function / homology
Function and homology information


canonical inflammasome complex / positive regulation of interleukin-18 production / pyroptotic inflammatory response / regulation of inflammatory response / defense response to virus / inflammatory response / innate immune response / ATP binding / cytoplasm
Similarity search - Function
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. ...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 / 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 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsPark, H.H. / Ha, H.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the human NLRP9 pyrin domain reveals a bent N-terminal loop that may regulate inflammasome assembly.
Authors: Ha, H.J. / Park, H.H.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 9


Theoretical massNumber of molelcules
Total (without water)12,8081
Polymers12,8081
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6510 Å2
Unit cell
Length a, b, c (Å)51.970, 33.685, 49.667
Angle α, β, γ (deg.)90.000, 102.397, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 9 / Nucleotide-binding oligomerization domain protein 6 / PYRIN and NACHT-containing protein 12


Mass: 12807.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP9, NALP9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7RTR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 1.66 Å3/Da / Density % sol: 25.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20%(w/v) PEG MME 2,000 0.1M Tris pH 8.5 0.2M Trimethylamine n-oxide

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→28.08 Å / Num. obs: 5035 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rsym value: 0.073 / Net I/σ(I): 22.28
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 306 / Rsym value: 0.533

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EWI

4ewi


Resolution: 2.08→28.08 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: FREE R-VALUE / ESU R: 0.326 / ESU R Free: 0.248
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2825 272 5.402 %
Rwork0.2133 --
all0.217 --
obs-5035 97.748 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.069 Å2
Baniso -1Baniso -2Baniso -3
1--1.624 Å2-0 Å22.149 Å2
2---0.397 Å20 Å2
3---0.982 Å2
Refinement stepCycle: LAST / Resolution: 2.08→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 14 800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013807
X-RAY DIFFRACTIONr_bond_other_d0.0320.017795
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.6391080
X-RAY DIFFRACTIONr_angle_other_deg2.1041.5951850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.12223.57142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.648153
X-RAY DIFFRACTIONr_chiral_restr0.1140.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02842
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02175
X-RAY DIFFRACTIONr_nbd_refined0.2310.2208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2430.2687
X-RAY DIFFRACTIONr_nbtor_refined0.1990.2400
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.219
X-RAY DIFFRACTIONr_nbd_other0.3140.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0350.22
X-RAY DIFFRACTIONr_mcbond_it4.0983.919358
X-RAY DIFFRACTIONr_mcbond_other4.0383.915357
X-RAY DIFFRACTIONr_mcangle_it4.9235.838444
X-RAY DIFFRACTIONr_mcangle_other4.9565.837445
X-RAY DIFFRACTIONr_scbond_it5.1594.324449
X-RAY DIFFRACTIONr_scbond_other5.1534.322450
X-RAY DIFFRACTIONr_scangle_it6.4856.344636
X-RAY DIFFRACTIONr_scangle_other6.486.342637
X-RAY DIFFRACTIONr_lrange_it7.00945.856990
X-RAY DIFFRACTIONr_lrange_other7.02945.83990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.083-2.1370.264150.262272X-RAY DIFFRACTION78.2016
2.137-2.1950.373180.216349X-RAY DIFFRACTION97.8667
2.195-2.2590.337230.213334X-RAY DIFFRACTION97.541
2.259-2.3280.392170.206315X-RAY DIFFRACTION100
2.328-2.4050.324240.193319X-RAY DIFFRACTION98.8473
2.405-2.4890.21130.203301X-RAY DIFFRACTION99.6825
2.489-2.5820.242160.203311X-RAY DIFFRACTION99.6951
2.582-2.6870.203170.236265X-RAY DIFFRACTION99.2958
2.687-2.8070.427140.222291X-RAY DIFFRACTION99.6732
2.807-2.9430.43390.199252X-RAY DIFFRACTION99.6183
2.943-3.1020.256220.214251X-RAY DIFFRACTION100
3.102-3.2890.279120.212240X-RAY DIFFRACTION100
3.289-3.5150.202140.225223X-RAY DIFFRACTION99.5798
3.515-3.7950.22120.207212X-RAY DIFFRACTION97.8166
3.795-4.1550.357100.213184X-RAY DIFFRACTION100
4.155-4.6410.12360.166183X-RAY DIFFRACTION99.4737
4.641-5.350.27120.228155X-RAY DIFFRACTION100
5.35-6.5330.477110.279135X-RAY DIFFRACTION100
6.533-9.1560.38850.217103X-RAY DIFFRACTION99.0826
9.156-28.080.06620.21368X-RAY DIFFRACTION100

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