+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0476 | |||||||||
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Title | Cryo-EM structure of NLRP3 bound to NEK7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Inflammasome / Activator / Biological process Immunity / Inflammatory response / Innate immunity / Transcription / Transcription regulation Ligand / ATP binding / Nucleotide binding / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / response to interferon-alpha / positive regulation of T-helper 2 cell differentiation ...NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / response to interferon-alpha / positive regulation of T-helper 2 cell differentiation / negative regulation of osteoblast proliferation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / regulation of hematopoietic progenitor cell differentiation / positive regulation of type 2 immune response / positive regulation of stress-activated MAPK cascade / cellular response to potassium ion / NLRP3 inflammasome complex / protein phosphatase regulator activity / Nuclear Pore Complex (NPC) Disassembly / peptidoglycan binding / SUMOylation of immune response proteins / osmosensory signaling pathway / regulation of hematopoietic stem cell proliferation / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / pattern recognition receptor signaling pathway / regulation of hematopoietic stem cell differentiation / negative regulation of interleukin-1 beta production / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / 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 / antiviral innate immune response / The NLRP3 inflammasome / protein maturation / spindle assembly / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / positive regulation of chemokine production / EML4 and NUDC in mitotic spindle formation / endoplasmic reticulum unfolded protein response / : / positive regulation of telomere maintenance via telomerase / regulation of mitotic cell cycle / cellular response to amino acid starvation / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / molecular function activator activity / non-specific protein-tyrosine kinase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / protein homooligomerization / Evasion by RSV of host interferon responses / Cytoprotection by HMOX1 / Metalloprotease DUBs / ISG15 antiviral mechanism / 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 / Interferon alpha/beta signaling / double-stranded RNA binding / protein-macromolecule adaptor activity / kinase activity / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / microtubule / defense response to virus / sequence-specific DNA binding / positive regulation of MAPK cascade / protein autophosphorylation / molecular adaptor activity / negative regulation of translation / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / inflammatory response / translation / negative regulation of cell population proliferation / Golgi membrane / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Sharif H / Wang L / Wu H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2019 Title: Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. Authors: Humayun Sharif / Li Wang / Wei Li Wang / Venkat Giri Magupalli / Liudmila Andreeva / Qi Qiao / Arthur V Hauenstein / Zhaolong Wu / Gabriel Núñez / Youdong Mao / Hao Wu / Abstract: The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation ...The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0476.map.gz | 48.4 MB | EMDB map data format | |
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Header (meta data) | emd-0476-v30.xml emd-0476.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0476_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_0476.png | 150.3 KB | ||
Filedesc metadata | emd-0476.cif.gz | 6.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0476 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0476 | HTTPS FTP |
-Validation report
Summary document | emd_0476_validation.pdf.gz | 523 KB | Display | EMDB validaton report |
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Full document | emd_0476_full_validation.pdf.gz | 522.6 KB | Display | |
Data in XML | emd_0476_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_0476_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0476 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0476 | HTTPS FTP |
-Related structure data
Related structure data | 6npyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0476.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : NL3-NEK7
Entire | Name: NL3-NEK7 |
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Components |
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-Supramolecule #1: NL3-NEK7
Supramolecule | Name: NL3-NEK7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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-Supramolecule #2: NLRP3
Supramolecule | Name: NLRP3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY ...Details: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY instead its IYCAKYRAY mutations were intended to introduce so that the class of MBP and NLRP3 is avoided |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: NEK7
Supramolecule | Name: NEK7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: NACHT, LRR and PYD domains-containing protein 3
Macromolecule | Name: NACHT, LRR and PYD domains-containing protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 117.890984 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR ...String: MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR LRLIKEHRSQ QEREQELLAI GKTKTCESPV SPIKMELLFD PDDEHSEPVH TVVFQGAAGI GKTILARKMM LD WASGTLY QDRFDYLFYI HCREVSLVTQ RSLGDLIMSC CPDPNPPIHK IVRKPSRILF LMDGFDELQG AFDEHIGPLC TDW QKAERG DILLSSLIRK KLLPEASLLI TTRPVALEKL QHLLDHPRHV EILGFSEAKR KEYFFKYFSD EAQARAAFSL IQEN EVLFT MCFIPLVCWI VCTGLKQQME SGKSLAQTSK TTTAVYVFFL SSLLQPRGGS QEHGLCAHLW GLCSLAADGI WNQKI LFEE SDLRNHGLQK ADVSAFLRMN LFQKEVDCEK FYSFIHMTFQ EFFAAMYYLL EEEKEGRTNV PGSRLKLPSR DVTVLL ENY GKFEKGYLIF VVRFLFGLVN QERTSYLEKK LSCKISQQIR LELLKWIEVK AKAKKLQIQP SQLELFYCLY EMQEEDF VQ RAMDYFPKIE INLSTRMDHM VSSFCIENCH RVESLSLGFL HNMPKEEEEE EKEGRHLDMV QCVLPSSSHA ACSHGLVN S HLTSSFCRGL FSVLSTSQSL TELDLSDNSL GDPGMRVLCE TLQHPGCNIR RLWLGRCGLS HECCFDISLV LSSNQKLVE LDLSDNALGD FGIRLLCVGL KHLLCNLKKL WLVSCCLTSA CCQDLASVLS TSHSLTRLYV GENALGDSGV AILCEKAKNP QCNLQKLGL VNSGLTSVCC SALSSVLSTN QNLTHLYLRG NTLGDKGIKL LCEGLLHPDC KLQVLELDNC NLTSHCCWDL S TLLTSSQS LRKLSLGNND LGDLGVMMFC EVLKQQSCLL QNLGLSEMYF NYETKSALET LQEEKPELTV VFEPSW UniProtKB: NACHT, LRR and PYD domains-containing protein 3 |
-Macromolecule #2: Protein kinase R,Serine/threonine-protein kinase Nek7
Macromolecule | Name: Protein kinase R,Serine/threonine-protein kinase Nek7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.01515 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT ...String: GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT AAHSLVGTPY YMSPERIHEN GYNFKSDIWS LGCLLYEMAA LQSPFYGDKM NLYSLCKKIE QCDYPPLPSD HY SEELRQL VNMCINPDPE KRPDVTYVYD VAKRMHACTA SS UniProtKB: Interferon-induced, double-stranded RNA-activated protein kinase, Serine/threonine-protein kinase Nek7 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.1 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6npy: |