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- EMDB-40855: Structure of NLRP3 and NEK7 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-40855
TitleStructure of NLRP3 and NEK7 complex
Map data
Sample
  • Complex: Covid Spike variant deltaN135
    • Protein or peptide: Serine/threonine-protein kinase Nek7
  • 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
KeywordsNLRP3 NEK7 complex / Cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


NEK6-subfamily protein kinase / small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / interphase microtubule organizing center / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production ...NEK6-subfamily protein kinase / small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / 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 / cellular response to potassium ion / Nuclear Pore Complex (NPC) Disassembly / 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 / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of NF-kappaB transcription factor activity / pyroptosis / positive regulation of telomere capping / 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 / spindle assembly / signaling adaptor activity / Purinergic signaling in leishmaniasis infection / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / regulation of mitotic cell cycle / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / molecular function activator activity / 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 / spindle pole / 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 / microtubule / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / centrosome / 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 / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Serine/threonine-protein kinase Nek7 / NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 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 22, 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_40855.png

Downloads & links

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Map

FileDownload / File: emd_40855.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-0.41144043 - 0.89332783
Average (Standard dev.)0.0023585095 (±0.027851572)
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_40855_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40855_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40855_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Covid Spike variant deltaN135

EntireName: Covid Spike variant deltaN135
Components
  • Complex: Covid Spike variant deltaN135
    • Protein or peptide: Serine/threonine-protein kinase Nek7
  • 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: Covid Spike variant deltaN135

SupramoleculeName: Covid Spike variant deltaN135 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Serine/threonine-protein kinase Nek7

MacromoleculeName: Serine/threonine-protein kinase Nek7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: NEK6-subfamily protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.603004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDEQSQGMQG PPVPQFQPQK ALRPDMGYNT LANFRIEKKI GRGQFSEVYR AACLLDGVPV ALMMVQIFDL MDAKARADCI KEIDLLKQL NHPNVIKYYA SFIEDNELNI VLELADAGDL SRMIKHFKKQ KRLIPERTVW KYFVQLCSAL EHMHSRRVMH R DIKPANVF ...String:
MDEQSQGMQG PPVPQFQPQK ALRPDMGYNT LANFRIEKKI GRGQFSEVYR AACLLDGVPV ALMMVQIFDL MDAKARADCI KEIDLLKQL NHPNVIKYYA SFIEDNELNI VLELADAGDL SRMIKHFKKQ KRLIPERTVW KYFVQLCSAL EHMHSRRVMH R DIKPANVF ITATGVVKLG DLGLGRFFSS KTTAAHSLVG TPYYMSPERI HENGYNFKSD IWSLGCLLYE MAALQSPFYG DK MNLYSLC KKIEQCDYPP LPSDHYSEEL RQLVNMCINP DPEKRPDVTY VYDVAKRMHA CTASS

UniProtKB: Serine/threonine-protein kinase Nek7

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Macromolecule #2: NACHT, LRR and PYD domains-containing protein 3

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: 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: 3 / Number of copies: 2 / 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 #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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: 7.5
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: 1.4000000000000001 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: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199924

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