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- PDB-8sxn: Structure of NLRP3 and NEK7 complex -

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Basic information

Entry
Database: PDB / ID: 8sxn
TitleStructure of NLRP3 and NEK7 complex
Components
  • NACHT, LRR and PYD domains-containing protein 3
  • Serine/threonine-protein kinase Nek7
KeywordsIMMUNE SYSTEM / NLRP3 NEK7 complex / Cryo-EM
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
Chem-7YN / ADENOSINE-5'-TRIPHOSPHATE / Serine/threonine-protein kinase Nek7 / NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsYu, X. / Matico, R.E. / Miller, R. / Schoubroeck, B.V. / Grauwen, K. / Suarez, J. / Pietrak, B. / Haloi, N. / Yin, Y. / Tresadern, G.J. ...Yu, X. / Matico, R.E. / Miller, R. / Schoubroeck, B.V. / Grauwen, K. / Suarez, J. / Pietrak, B. / Haloi, N. / Yin, Y. / Tresadern, G.J. / Perez-Benito, L. / Lindahl, E. / Bottelbergs, A. / Oehlrich, D. / Opdenbosch, N.V. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of NLRP3 reveal its self-activation mechanism
Authors: Yu, X. / Matico, R.E. / Miller, R. / Schoubroeck, B.V. / Grauwen, K. / Suarez, J. / Pietrak, B. / Haloi, N. / Yin, Y. / Tresadern, G.J. / Perez-Benito, L. / Lindahl, E. / Bottelbergs, A. / ...Authors: Yu, X. / Matico, R.E. / Miller, R. / Schoubroeck, B.V. / Grauwen, K. / Suarez, J. / Pietrak, B. / Haloi, N. / Yin, Y. / Tresadern, G.J. / Perez-Benito, L. / Lindahl, E. / Bottelbergs, A. / Oehlrich, D. / Opdenbosch, N.V. / Sharma, S.
History
DepositionMay 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek7
B: Serine/threonine-protein kinase Nek7
C: NACHT, LRR and PYD domains-containing protein 3
D: NACHT, LRR and PYD domains-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,3798
Polymers276,5594
Non-polymers1,8194
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine/threonine-protein kinase Nek7 / Never in mitosis A-related kinase 7 / NimA-related protein kinase 7


Mass: 34603.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDX7, NEK6-subfamily protein kinase
#2: 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: 103676.641 Da / Num. of mol.: 2
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, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Chemical ChemComp-7YN / 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea


Mass: 402.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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: Covid Spike variant deltaN135 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199924 / Symmetry type: POINT

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