+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40855 | |||||||||
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Title | Structure of NLRP3 and NEK7 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NLRP3 NEK7 complex / Cryo-EM / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information NEK6-subfamily protein kinase / small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production ...NEK6-subfamily protein kinase / small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / cellular response to potassium ion / NLRP3 inflammasome complex / Nuclear Pore Complex (NPC) Disassembly / 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 NLRP3 inflammasome complex assembly / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / pyroptotic inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of telomere capping / negative regulation of acute inflammatory response / The NLRP3 inflammasome / protein maturation / spindle assembly / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / EML4 and NUDC in mitotic spindle formation / : / 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 / 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 / spindle pole / 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 / microtubule / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / protein phosphorylation / innate immune response / protein serine kinase activity / 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 / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.04 Å | |||||||||
Authors | Yu 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 support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40855.map.gz | 167.8 MB | EMDB map data format | |
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Header (meta data) | emd-40855-v30.xml emd-40855.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_40855.png | 59.8 KB | ||
Filedesc metadata | emd-40855.cif.gz | 6.4 KB | ||
Others | emd_40855_additional_1.map.gz emd_40855_half_map_1.map.gz emd_40855_half_map_2.map.gz | 87.5 MB 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40855 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40855 | HTTPS FTP |
-Validation report
Summary document | emd_40855_validation.pdf.gz | 898.4 KB | Display | EMDB validaton report |
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Full document | emd_40855_full_validation.pdf.gz | 898 KB | Display | |
Data in XML | emd_40855_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_40855_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40855 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40855 | HTTPS FTP |
-Related structure data
Related structure data | 8sxnMC 8swfC 8swkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40855.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40855_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40855_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40855_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Covid Spike variant deltaN135
Entire | Name: Covid Spike variant deltaN135 |
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Components |
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-Supramolecule #1: Covid Spike variant deltaN135
Supramolecule | Name: Covid Spike variant deltaN135 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Serine/threonine-protein kinase Nek7
Macromolecule | Name: Serine/threonine-protein kinase Nek7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: NEK6-subfamily protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.603004 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: NACHT, LRR and PYD domains-containing protein 3
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 103.676641 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #3: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrah...
Macromolecule | Name: 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 |
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Molecular weight | Theoretical: 402.464 Da |
Chemical component information | ChemComp-7YN: |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199924 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |