+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28175 | |||||||||
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Title | Cryo-EM structure of the active NLRP3 inflammasome disk | |||||||||
Map data | Primary Map | |||||||||
Sample |
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Keywords | Inflammasome / CYTOSOLIC PROTEIN / Immune System-Transferase complex | |||||||||
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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Hao W / Le X | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Cryo-EM structures of the active NLRP3 inflammasome disc. Authors: Le Xiao / Venkat Giri Magupalli / Hao Wu / Abstract: Inflammasomes are cytosolic innate immune complexes that activate caspase-1 following detection of pathogenic and endogenous dangers, and NACHT-, leucine-rich repeat (LRR)- and pyrin domain (PYD)- ...Inflammasomes are cytosolic innate immune complexes that activate caspase-1 following detection of pathogenic and endogenous dangers, and NACHT-, leucine-rich repeat (LRR)- and pyrin domain (PYD)-containing protein 3 (NLRP3) is an inflammasome sensor of membrane damage highly important in regard to the induction of inflammation. Here we report cryogenic electron microscopy structures of disc-shaped active NLRP3 oligomers in complex with adenosine 5'-O-(3-thio)triphosphate, the centrosomal NIMA-related kinase 7 (NEK7) and the adaptor protein ASC, which recruits caspase-1. In these NLRP3-NEK7-ASC complexes, the central NACHT domain of NLRP3 assumes an ATP-bound conformation in which two of its subdomains rotate by about 85° relative to the ADP-bound inactive conformation. The fish-specific NACHT-associated domain conserved in NLRP3 but absent in most NLRPs becomes ordered in its key regions to stabilize the active NACHT conformation and mediate most interactions in the disc. Mutations on these interactions compromise NLRP3-mediated caspase-1 activation. The N-terminal PYDs from all NLRP3 subunits combine to form a PYD filament that recruits ASC PYD to elicit downstream signalling. Surprisingly, the C-terminal LRR domain and the LRR-bound NEK7 do not participate in disc interfaces. Together with previous structures of an inactive NLRP3 cage in which LRR-LRR interactions play an important role, we propose that the role of NEK7 is to break the inactive cage to transform NLRP3 into the active NLRP3 inflammasome disc. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28175.map.gz | 483.2 MB | EMDB map data format | |
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Header (meta data) | emd-28175-v30.xml emd-28175.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_28175.png | 232.6 KB | ||
Filedesc metadata | emd-28175.cif.gz | 6.1 KB | ||
Others | emd_28175_half_map_1.map.gz emd_28175_half_map_2.map.gz | 473.9 MB 473.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28175 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28175 | HTTPS FTP |
-Validation report
Summary document | emd_28175_validation.pdf.gz | 992.9 KB | Display | EMDB validaton report |
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Full document | emd_28175_full_validation.pdf.gz | 992.5 KB | Display | |
Data in XML | emd_28175_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_28175_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28175 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28175 | HTTPS FTP |
-Related structure data
Related structure data | 8ej4MC 8ertC 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_28175.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Primary Map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map 1
File | emd_28175_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_28175_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : a complex of NLRP3 and NEK7
Entire | Name: a complex of NLRP3 and NEK7 |
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Components |
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-Supramolecule #1: a complex of NLRP3 and NEK7
Supramolecule | Name: a complex of NLRP3 and NEK7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#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: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 102.67557 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KKDYRKKYRK YVRSRFQCIE DRNARLGESV SLNKRYTRLR LIKEHRSQQE REQELLAIGK TKTCESPVSP IKMELLFDPD DEHSEPVHT VVFQGAAGIG KTILARKMML DWASGTLYQD RFDYLFYIHC REVSLVTQRS LGDLIMSCCP DPNPPIHKIV R KPSRILFL ...String: KKDYRKKYRK YVRSRFQCIE DRNARLGESV SLNKRYTRLR LIKEHRSQQE REQELLAIGK TKTCESPVSP IKMELLFDPD DEHSEPVHT VVFQGAAGIG KTILARKMML DWASGTLYQD RFDYLFYIHC REVSLVTQRS LGDLIMSCCP DPNPPIHKIV R KPSRILFL MDGFDELQGA FDEHIGPLCT DWQKAERGDI LLSSLIRKKL LPEASLLITT RPVALEKLQH LLDHPRHVEI LG FSEAKRK EYFFKYFSDE AQARAAFSLI QENEVLFTMC FIPLVCWIVC TGLKQQMESG KSLAQTSKTT TAVYVFFLSS LLQ PRGGSQ EHGLCAHLWG LCSLAADGIW NQKILFEESD LRNHGLQKAD VSAFLRMNLF QKEVDCEKFY SFIHMTFQEF FAAM YYLLE EEKEGRTNVP GSRLKLPSRD VTVLLENYGK FEKGYLIFVV RFLFGLVNQE RTSYLEKKLS CKISQQIRLE LLKWI EVKA KAKKLQIQPS QLELFYCLYE MQEEDFVQRA MDYFPKIEIN LSTRMDHMVS SFCIENCHRV ESLSLGFLHN MPKEEE EEE KEGRHLDMVQ CVLPSSSHAA CSHGLVNSHL TSSFCRGLFS VLSTSQSLTE LDLSDNSLGD PGMRVLCETL QHPGCNI RR LWLGRCGLSH ECCFDISLVL SSNQKLVELD LSDNALGDFG IRLLCVGLKH LLCNLKKLWL VSCCLTSACC QDLASVLS T SHSLTRLYVG ENALGDSGVA ILCEKAKNPQ CNLQKLGLVN SGLTSVCCSA LSSVLSTNQN LTHLYLRGNT LGDKGIKLL CEGLLHPDCK LQVLELDNCN LTSHCCWDLS TLLTSSQSLR KLSLGNNDLG DLGVMMFCEV LKQQSCLLQN LGLSEMYFNY ETKSALETL QEEKPELTVV FEP UniProtKB: NACHT, LRR and PYD domains-containing protein 3 |
-Macromolecule #2: Serine/threonine-protein kinase Nek7
Macromolecule | Name: Serine/threonine-protein kinase Nek7 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.038203 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KALRPDMGYN TLANFRIEKK IGRGQFSEVY RAACLLDGVP VALKKVQIFD LMDAKARADC IKEIDLLKQL NHPNVIKYYA SFIEDNELN IVLELADAGD LSRMIKHFKK QKRLIPERTV WKYFVQLCSA LEHMHSRRVM HRDIKPANVF ITATGVVKLG D LGLGRFFS ...String: KALRPDMGYN TLANFRIEKK IGRGQFSEVY RAACLLDGVP VALKKVQIFD LMDAKARADC IKEIDLLKQL NHPNVIKYYA SFIEDNELN IVLELADAGD LSRMIKHFKK QKRLIPERTV WKYFVQLCSA LEHMHSRRVM HRDIKPANVF ITATGVVKLG D LGLGRFFS SKTTAAHSLV GTPYYMSPER IHENGYNFKS DIWSLGCLLY EMAALQSPFY GDKMNLYSLC KKIEQCDYPP LP SDHYSEE LRQLVNMCIN PDPEKRPDVT YVYDVAKRMH A UniProtKB: Serine/threonine-protein kinase Nek7 |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 10 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 50.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51576 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |