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- PDB-9ihn: Cryo-EM structure of NLRP3 bound to the inhibitor BAL-1516 at 3.0... -

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Basic information

Entry
Database: PDB / ID: 9ihn
TitleCryo-EM structure of NLRP3 bound to the inhibitor BAL-1516 at 3.06 Ang resolution
ComponentsNACHT, LRR and PYD domains-containing protein 3
KeywordsIMMUNE SYSTEM / NLRP3 / NOD-like receptor / BAL compound / inhibitor / inflammasome / BAL-1516
Function / homology
Function and homology information


detection of biotic stimulus / molecular sensor activity / positive regulation of type 2 immune response / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 2 cell cytokine production / interphase microtubule organizing center / NLRP3 inflammasome complex / peptidoglycan binding / NLRP3 inflammasome complex assembly ...detection of biotic stimulus / molecular sensor activity / positive regulation of type 2 immune response / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 2 cell cytokine production / interphase microtubule organizing center / NLRP3 inflammasome complex / peptidoglycan binding / NLRP3 inflammasome complex assembly / cysteine-type endopeptidase activator activity / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / osmosensory signaling pathway / negative regulation of interleukin-1 beta production / positive regulation of interleukin-4 production / pattern recognition receptor signaling pathway / negative regulation of acute inflammatory response / microtubule organizing center / The NLRP3 inflammasome / pyroptotic inflammatory response / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / positive regulation of interleukin-1 beta production / cellular response to virus / protein maturation / defense response / Cytoprotection by HMOX1 / molecular condensate scaffold activity / negative regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of inflammatory response / Metalloprotease DUBs / SARS-CoV-1 activates/modulates innate immune responses / cellular response to lipopolysaccharide / regulation of inflammatory response / DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / protein-macromolecule adaptor activity / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA-templated transcription / extracellular region / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
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 profile. / NACHT nucleoside triphosphatase ...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 profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / 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 / NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsTorp, J. / Wilhelmsen, K. / Hartman, G. / Hagelueken, G. / Geyer, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GE 976/16-1 Germany
German Research Foundation (DFG)EXC2151-390873048 Germany
CitationJournal: To Be Published
Title: Inhibition of NLRP3 by a CNS-penetrating indazole scaffold
Authors: Torp, J. / Geyer, M.
History
DepositionFeb 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2114
Polymers118,3241
Non-polymers8873
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NACHT, LRR and PYD domains-containing protein 3 / Angiotensin/vasopressin receptor AII/AVP-like / Caterpiller protein 1.1 / CLR1.1 / Cold-induced ...Angiotensin/vasopressin receptor AII/AVP-like / Caterpiller protein 1.1 / CLR1.1 / Cold-induced autoinflammatory syndrome 1 protein / Cryopyrin / PYRIN-containing APAF1-like protein 1


Mass: 118323.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP3, C1orf7, CIAS1, NALP3, PYPAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96P20
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-A1I4G / 3-ethoxy-~{N}-methyl-~{N}-[(1~{R})-1-(4-methyl-1~{H}-pyrazolo[4,3-c]pyridin-7-yl)ethyl]-4-(4-methyl-1,3-thiazol-2-yl)benzamide


Mass: 435.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N5O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of human NLRP3 bound to the inhibitor BAL-1516
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES1
2150 mMsodium chlorideNaCl1
310 mMmagnesium chlorideMgCl21
40.5 mMTCEP1
51 mMADP1
60.01 mMBAL-15161
SpecimenConc.: 0.78 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51.7 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 765958 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036843
ELECTRON MICROSCOPYf_angle_d0.5289234
ELECTRON MICROSCOPYf_dihedral_angle_d5.323912
ELECTRON MICROSCOPYf_chiral_restr0.0381040
ELECTRON MICROSCOPYf_plane_restr0.0031161

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