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- EMDB-40820: Cryo-EM structure of NLRP3 closed hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-40820
TitleCryo-EM structure of NLRP3 closed hexamer
Map data
Sample
  • Complex: NLRP3 open octamer complex
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
  • Ligand: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsClosed NLRP3 / Cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


molecular 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 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / osmosensory signaling pathway ...molecular 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 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / osmosensory signaling pathway / positive regulation of type 2 immune response / pattern recognition receptor 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 / pyroptotic inflammatory response / positive regulation of interleukin-4 production / negative regulation of acute inflammatory response / The NLRP3 inflammasome / protein maturation / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / Cytoprotection by HMOX1 / cellular response to virus / Metalloprotease DUBs / negative regulation of inflammatory response / defense response / 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 / protein-macromolecule adaptor 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / identical protein binding / membrane / 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 / 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 / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / 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: 4.32 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_40820.png

Downloads & links

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Map

FileDownload / File: emd_40820.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.181
Minimum - Maximum-0.8600413 - 1.238975
Average (Standard dev.)0.0048301816 (±0.039206635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40820_additional_1.map
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Half map: #1

Fileemd_40820_half_map_1.map
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Histogram

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Half map: #2

Fileemd_40820_half_map_2.map
Projections & Slices
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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
  • Ligand: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: NLRP3 open octamer complex

SupramoleculeName: NLRP3 open octamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 6 / 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: 103.676641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AEYCFNKKDY RKKYRKYVRS RFQCIEDRNA RLGESVSLNK RYTRLRLIKE HRSQQEREQE LLAIGKTKTC ESPVSPIKME LLFDPDDEH SEPVHTVVFQ GAAGIGKTIL ARKMMLDWAS GTLYQDRFDY LFYIHCREVS LVTQRSLGDL IMSCCPDPNP P IHKIVRKP ...String:
AEYCFNKKDY 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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Macromolecule #2: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrah...

MacromoleculeName: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea
type: ligand / ID: 2 / Number of copies: 6 / Formula: 7YN
Molecular weightTheoretical: 402.464 Da
Chemical component information

ChemComp-7YN:
1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72861
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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