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- EMDB-40811: Cryo-EM structure of NLRP3 open octamer -

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Basic information

Entry
Database: EMDB / ID: EMD-40811
TitleCryo-EM structure of NLRP3 open octamer
Map data
Sample
  • Complex: NLRP3 open octamer complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
KeywordsActivated NLRP3 / Cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / interphase microtubule organizing center / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response ...small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / interphase microtubule organizing center / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response / osmosensory signaling pathway / peptidoglycan binding / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / microtubule organizing center / negative regulation of interleukin-1 beta production / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pyroptosis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein maturation / The NLRP3 inflammasome / negative regulation of acute inflammatory response / positive regulation of interleukin-4 production / signaling adaptor activity / Purinergic signaling in leishmaniasis infection / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / defense response / Cytoprotection by HMOX1 / Metalloprotease DUBs / negative regulation of inflammatory response / cellular response to virus / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / 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 / 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 / Leucine rich repeat, ribonuclease inhibitor type / DAPIN domain / DAPIN domain profile. ...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 / Leucine rich repeat, ribonuclease inhibitor type / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsYu X / Matico RE / Miller R / Schoubroeck BV / Grauwen K / Suarez J / Pietrak B / Haloi N / Yin Y / Tresadern GJ ...Yu X / Matico RE / Miller R / Schoubroeck BV / Grauwen K / Suarez J / Pietrak B / Haloi N / Yin Y / Tresadern GJ / Perez-Benito L / Lindahl E / Bottelbergs A / Oehlrich D / Opdenbosch NV / Sharma S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of NLRP3 reveal its self-activation mechanism
Authors: Yu X / Matico RE / Miller R / Schoubroeck BV / Grauwen K / Suarez J / Pietrak B / Haloi N / Yin Y / Tresadern GJ / Perez-Benito L / Lindahl E / Bottelbergs A / Oehlrich D / Opdenbosch NV / Sharma S
History
DepositionMay 18, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40811.png

Downloads & links

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Map

FileDownload / File: emd_40811.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.5072232 - 2.360269
Average (Standard dev.)0.012855496 (±0.07794462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40811_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40811_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40811_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : NLRP3 open octamer complex

EntireName: NLRP3 open octamer complex
Components
  • Complex: NLRP3 open octamer complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3

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Supramolecule #1: NLRP3 open octamer complex

SupramoleculeName: NLRP3 open octamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.675742 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AEYCKMKKDY RKKYRKYVRS RFQCIEDRNA RLGESVSLNK RYTRLRLIKE HRSQQEREQE LLAIGKTKTC ESPVSPIKME LLFDPDDEH SEPVHTVVFQ GAAGIGKTIL ARKMMLDWAS GTLYQDRFDY LFYIHCREVS LVTQRSLGDL IMSCCPDPNP P IHKIVRKP ...String:
AEYCKMKKDY RKKYRKYVRS RFQCIEDRNA RLGESVSLNK RYTRLRLIKE HRSQQEREQE LLAIGKTKTC ESPVSPIKME LLFDPDDEH SEPVHTVVFQ GAAGIGKTIL ARKMMLDWAS GTLYQDRFDY LFYIHCREVS LVTQRSLGDL IMSCCPDPNP P IHKIVRKP SRILFLMDGF DELQGAFDEH IGPLCTDWQK AERGDILLSS LIRKKLLPEA SLLITTRPVA LEKLQHLLDH PR HVEILGF SEAKRKEYFF KYFSDEAQAR AAFSLIQENE VLFTMCFIPL VCWIVCTGLK QQMESGKSLA QTSKTTTAVY VFF LSSLLQ PRGGSQEHGL CAHLWGLCSL AADGIWNQKI LFEESDLRNH GLQKADVSAF LRMNLFQKEV DCEKFYSFIH MTFQ EFFAA MYYLLEEEKE GRTNVPGSRL KLPSRDVTVL LENYGKFEKG YLIFVVRFLF GLVNQERTSY LEKKLSCKIS QQIRL ELLK WIEVKAKAKK LQIQPSQLEL FYCLYEMQEE DFVQRAMDYF PKIEINLSTR MDHMVSSFCI ENCHRVESLS LGFLHN MPK EEEEEEKEGR HLDMVQCVLP SSSHAACSHG LVNSHLTSSF CRGLFSVLST SQSLTELDLS DNSLGDPGMR VLCETLQ HP GCNIRRLWLG RCGLSHECCF DISLVLSSNQ KLVELDLSDN ALGDFGIRLL CVGLKHLLCN LKKLWLVSCC LTSACCQD L ASVLSTSHSL TRLYVGENAL GDSGVAILCE KAKNPQCNLQ KLGLVNSGLT SVCCSALSSV LSTNQNLTHL YLRGNTLGD KGIKLLCEGL LHPDCKLQVL ELDNCNLTSH CCWDLSTLLT SSQSLRKLSL GNNDLGDLGV MMFCEVLKQQ SCLLQNLGLS EMYFNYETK SALETLQEEK PELTVVFEPS W

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 466664

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