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- EMDB-13686: High resolution reconstruction of the human NLRP3 decamer -

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Basic information

Entry
Database: EMDB / ID: EMD-13686
TitleHigh resolution reconstruction of the human NLRP3 decamer
Map dataHigh resolution reconstruction of the human NLRP3 decamer.
Sample
  • Complex: Decamer of human NLRP3
    • Protein or peptide: NLRP3
KeywordsInflammasome / innate immunity / IMMUNE SYSTEM
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
NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHochheiser IV / Pilsl M / Hagelueken G / Engel C / Geyer M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC2151-390873048 Germany
CitationJournal: Nature / Year: 2022
Title: Structure of the NLRP3 decamer bound to the cytokine release inhibitor CRID3.
Authors: Inga V Hochheiser / Michael Pilsl / Gregor Hagelueken / Jonas Moecking / Michael Marleaux / Rebecca Brinkschulte / Eicke Latz / Christoph Engel / Matthias Geyer /
Abstract: NLRP3 is an intracellular sensor protein that when activated by a broad spectrum of exogenous and endogenous stimuli leads to inflammasome formation and pyroptosis. The conformational states of NLRP3 ...NLRP3 is an intracellular sensor protein that when activated by a broad spectrum of exogenous and endogenous stimuli leads to inflammasome formation and pyroptosis. The conformational states of NLRP3 and the way antagonistic small molecules act at the molecular level remain poorly understood. Here we report the cryo-electron microscopy structures of full-length human NLRP3 in its native form and complexed with the inhibitor CRID3 (also named MCC950). Inactive, ADP-bound NLRP3 is a decamer composed of homodimers of intertwined leucine-rich repeat (LRR) domains that assemble back-to-back as pentamers. The NACHT domain is located at the apical axis of this spherical structure. One pyrin domain dimer is in addition formed inside the LRR cage. Molecular contacts between the concave sites of two opposing LRR domains are mediated by an acidic loop that extends from an LRR transition segment. Binding of CRID3 considerably stabilizes the NACHT and LRR domains relative to each other. CRID3 binds into a cleft, connecting four subdomains of the NACHT with the transition LRR. Its central sulfonylurea group interacts with the Walker A motif of the NLRP3 nucleotide-binding domain and is sandwiched between two arginine residues, which explains the specificity of NLRP3 for this chemical entity. With the determination of the binding site of this key therapeutic agent, specific targeting of NLRP3 for the treatment of autoinflammatory and autoimmune diseases and rational drug optimization is within reach.
History
DepositionOct 7, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pzc
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13686.png

Downloads & links

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Map

FileDownload / File: emd_13686.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHigh resolution reconstruction of the human NLRP3 decamer.
Voxel sizeX=Y=Z: 1.29 Å
Density
Contour LevelBy AUTHOR: 0.00515 / Movie #1: 0.006
Minimum - Maximum-0.021310026 - 0.046460148
Average (Standard dev.)0.00019432575 (±0.0017140794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0210.0460.000

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Supplemental data

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Sample components

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Entire : Decamer of human NLRP3

EntireName: Decamer of human NLRP3
Components
  • Complex: Decamer of human NLRP3
    • Protein or peptide: NLRP3

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Supramolecule #1: Decamer of human NLRP3

SupramoleculeName: Decamer of human NLRP3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: NLRP3

MacromoleculeName: NLRP3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKMASTRCKL ARYLEDLEDV DLKKFKMHLE DYPPQKGCIP LPRGQTEKAD HVDLATLMID FNGEEKAWA MAVWIFAAIN RRDLYEKAKR DEPKWGSDNA RVSNPTVICQ EDSIEEEWMG L LEYLSRIS ICKMKKDYRK KYRKYVRSRF QCIEDRNARL GESVSLNKRY ...String:
MKMASTRCKL ARYLEDLEDV DLKKFKMHLE DYPPQKGCIP LPRGQTEKAD HVDLATLMID FNGEEKAWA MAVWIFAAIN RRDLYEKAKR DEPKWGSDNA RVSNPTVICQ EDSIEEEWMG L LEYLSRIS ICKMKKDYRK KYRKYVRSRF QCIEDRNARL GESVSLNKRY TRLRLIKEHR SQ QEREQEL LAIGKTKTCE SPVSPIKMEL LFDPDDEHSE PVHTVVFQGA AGIGKTILAR KMM LDWASG TLYQDRFDYL FYIHCREVSL VTQRSLGDLI MSCCPDPNPP IHKIVRKPSR ILFL MDGFD ELQGAFDEHI GPLCTDWQKA ERGDILLSSL IRKKLLPEAS LLITTRPVAL EKLQH LLDH PRHVEILGFS EAKRKEYFFK YFSDEAQARA AFSLIQENEV LFTMCFIPLV CWIVCT GLK QQMESGKSLA QTSKTTTAVY VFFLSSLLQP RGGSQEHGLC AHLWGLCSLA ADGIWNQ KI LFEESDLRNH GLQKADVSAF LRMNLFQKEV DCEKFYSFIH MTFQEFFAAM YYLLEEEK E GRTNVPGSRL KLPSRDVTVL LENYGKFEKG YLIFVVRFLF GLVNQERTSY LEKKLSCKI SQQIRLELLK WIEVKAKAKK LQIQPSQLEL FYCLYEMQEE DFVQRAMDYF PKIEINLSTR MDHMVSSFC IENCHRVESL SLGFLHNMPK EEEEEEKEGR HLDMVQCVLP SSSHAACSHG L VNSHLTSS FCRGLFSVLS TSQSLTELDL SDNSLGDPGM RVLCETLQHP GCNIRRLWLG RC GLSHECC FDISLVLSSN QKLVELDLSD NALGDFGIRL LCVGLKHLLC NLKKLWLVSC CLT SACCQD LASVLSTSHS LTRLYVGENA LGDSGVAILC EKAKNPQCNL QKLGLVNSGL TSVC CSALS SVLSTNQNLT HLYLRGNTLG DKGIKLLCEG LLHPDCKLQV LELDNCNLTS HCCWD LSTL LTSSQSLRKL SLGNNDLGDL GVMMFCEVLK QQSCLLQNLG LSEMYFNYET KSALET LQE EKPELTVVFE PSW

UniProtKB: NACHT, LRR and PYD domains-containing protein 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
Detailspurified protein

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 161351
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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