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- PDB-6z2g: Crystal structure of human NLRP9 PYD -

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Basic information

Entry
Database: PDB / ID: 6z2g
TitleCrystal structure of human NLRP9 PYD
ComponentsNACHT, LRR and PYD domains-containing protein 9
KeywordsIMMUNE SYSTEM / Inflammasome / Pyrin domain / PYD / NLRP9
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 / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT 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 / Death Domain, Fas / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Death Domain, Fas / Leucine Rich repeat / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
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: 1.95 Å
AuthorsMarleaux, M. / Anand, K. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)2014_A203 Germany
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly.
Authors: Marleaux, M. / Anand, K. / Latz, E. / Geyer, M.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _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)11,9791
Polymers11,9791
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.330, 33.330, 311.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 11978.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP9, NALP9, NOD6, PAN12 / Plasmid: pGex4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7RTR0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: Hexagonal shaped
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Bicine pH 9.0, 0.2 M sodium thiocyanate, 0.1 M sodium formate, and 25-27% v/w PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0000089 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000089 Å / Relative weight: 1
ReflectionResolution: 1.95→29 Å / Num. obs: 14097 / % possible obs: 99.5 % / Redundancy: 22 % / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.082 / Rsym value: 0.08 / Net I/σ(I): 18.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 16 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2285 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.24 / Rrim(I) all: 1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ewi

4ewi


Resolution: 1.95→28.86 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 35.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 706 5.01 %Random
Rwork0.2155 13391 --
obs0.216 14097 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.45 Å2 / Biso mean: 67.3525 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 1.95→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 0 16 790
Biso mean---75.11 -
Num. residues----89
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.10.38241420.35152672281499
2.1-2.310.36661410.27652652279399
2.31-2.640.31821390.262726742813100
2.64-3.330.24181410.271427112852100
3.33-28.860.18311430.178826822825100
Refinement TLS params.Method: refined / Origin x: -9.9667 Å / Origin y: -12.0534 Å / Origin z: 10.4364 Å
111213212223313233
T0.4398 Å2-0.0288 Å20.0136 Å2-0.4822 Å20.0162 Å2--0.4299 Å2
L4.4792 °20.5543 °20.1394 °2-4.3751 °2-3.0475 °2--6.2365 °2
S-0.2844 Å °0.1485 Å °0.1265 Å °-0.1992 Å °0.1797 Å °0.1675 Å °0.2751 Å °-0.3042 Å °0.1513 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 97
2X-RAY DIFFRACTION1allS1 - 17

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