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- PDB-8wsm: NLRP3 NACHT domain in complex with compound 32 -

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Basic information

Entry
Database: PDB / ID: 8wsm
TitleNLRP3 NACHT domain in complex with compound 32
ComponentsNACHT, LRR and PYD domains-containing protein 3
KeywordsIMMUNE SYSTEM / inflammasome
Function / homology
Function and homology information


small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / NLRP3 inflammasome complex ...small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / NLRP3 inflammasome complex / peptidoglycan binding / osmosensory signaling pathway / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / pattern recognition receptor signaling pathway / negative regulation of interleukin-1 beta production / microtubule organizing center / positive regulation of interleukin-4 production / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of acute inflammatory response / The NLRP3 inflammasome / protein maturation / Purinergic signaling in leishmaniasis infection / 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 / Cytoprotection by HMOX1 / Metalloprotease DUBs / cellular response to virus / ADP binding / defense response / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / SARS-CoV-1 activates/modulates innate immune responses / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated 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-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated 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 / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-XE3 / NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAkai, S. / Orita, T. / Adachi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of Novel NLRP3 Inflammasome Inhibitors Composed of an Oxazole Scaffold Bearing an Acylsulfamide.
Authors: Ohba, Y. / Adachi, K. / Furukawa, T. / Nishimaru, T. / Sakurai, K. / Masuo, R. / Inami, T. / Orita, T. / Akai, S. / Adachi, T. / Usui, K. / Hamada, Y. / Mori, M. / Kurimoto, T. / Wakashima, ...Authors: Ohba, Y. / Adachi, K. / Furukawa, T. / Nishimaru, T. / Sakurai, K. / Masuo, R. / Inami, T. / Orita, T. / Akai, S. / Adachi, T. / Usui, K. / Hamada, Y. / Mori, M. / Kurimoto, T. / Wakashima, T. / Akiyama, Y. / Miyazaki, S. / Noji, S.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0564
Polymers64,1561
Non-polymers9003
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-18 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.997, 96.997, 266.057
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 3


Mass: 64156.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP3 / Production host: unidentified baculovirus / References: UniProt: Q96P20
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-XE3 / 2-[[2-methyl-5-(trifluoromethyl)phenyl]amino]-~{N}-(1,4-oxazepan-4-ylsulfonyl)-1,3-oxazole-4-carboxamide


Mass: 448.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19F3N4O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5, 1.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→84 Å / Num. obs: 21147 / % possible obs: 99.79 % / Redundancy: 2 % / Biso Wilson estimate: 69.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.016 / Rrim(I) all: 0.023 / Net I/σ(I): 17.03
Reflection shellResolution: 2.7→2.799 Å / Redundancy: 2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 2032 / CC1/2: 0.912 / Rpim(I) all: 0.23 / Rrim(I) all: 0.32 / % possible all: 98.98

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→84 Å / SU ML: 0.376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 972 4.6 %
Rwork0.2132 20154 -
obs0.2149 21126 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 58 17 3967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274037
X-RAY DIFFRACTIONf_angle_d0.51465436
X-RAY DIFFRACTIONf_chiral_restr0.0356590
X-RAY DIFFRACTIONf_plane_restr0.0033671
X-RAY DIFFRACTIONf_dihedral_angle_d11.51081519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.850.39181140.30562794X-RAY DIFFRACTION99.25
2.85-3.020.34361340.28532815X-RAY DIFFRACTION99.9
3.02-3.260.28981430.25242815X-RAY DIFFRACTION99.93
3.26-3.580.24761270.22372849X-RAY DIFFRACTION99.93
3.58-4.10.25381380.2042870X-RAY DIFFRACTION99.93
4.1-5.170.1841490.17662903X-RAY DIFFRACTION99.93
5.17-840.26021670.20933108X-RAY DIFFRACTION99.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.65199962132-2.63636044451-1.683674815093.76751244618-2.938271055359.35600752209-0.0335596694665-0.6036090403020.4490763013210.2063112128140.190947232509-0.458029889565-0.1319953490260.932114515357-0.1575954652930.589423632016-0.170417487591-0.07540602955390.847939502907-0.2563969270330.72068071571420.345334165544.9499567541150.199418805
22.26551292252-1.39164891114-1.959756645781.248705448431.700107457983.77403370355-0.125289230479-0.192625724992-0.05233765003560.2532643477990.0590335089690.04221080866040.5090618145150.1902552261120.02781955239670.510411364545-0.06686661354240.06615353368590.483704910403-0.08213014439270.62294911535215.546129596237.9528679464142.046856197
32.594909651770.430759328274-0.5232225818754.01391635582-1.259440999676.1430078722-0.106007591440.161332136615-0.5149549466410.141665535917-0.1495045344010.2654784212610.975947488551-0.2496272110720.2759748137820.693920619512-0.07173641459650.1274126087560.617644732962-0.2241005145740.87083316234311.600068827125.2095498448124.045048174
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 134 through 220 )134 - 2201 - 51
22chain 'A' and (resid 221 through 465 )221 - 46552 - 285
33chain 'A' and (resid 466 through 676 )466 - 676286 - 472

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