+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32120 | |||||||||||||||
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Title | Cryo-EM structure of mouse NLRP3 (full-length) dodecamer | |||||||||||||||
Map data | cryo-EM map of mouse NLRP3 dodecamer | |||||||||||||||
Sample |
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Function / homology | Function and homology information The NLRP3 inflammasome / positive regulation of T-helper 17 cell differentiation / small molecule sensor activity / detection of biotic stimulus / Metalloprotease DUBs / phosphatidylinositol phosphate binding / positive regulation of cytokine production involved in immune response / positive regulation of T-helper 2 cell differentiation / canonical inflammasome complex / NLRP3 inflammasome complex assembly ...The NLRP3 inflammasome / positive regulation of T-helper 17 cell differentiation / small molecule sensor activity / detection of biotic stimulus / Metalloprotease DUBs / phosphatidylinositol phosphate binding / positive regulation of cytokine production involved in immune response / positive regulation of T-helper 2 cell differentiation / canonical inflammasome complex / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / acute inflammatory response / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / NLRP3 inflammasome complex / leukocyte migration involved in inflammatory response / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / cellular response to peptidoglycan / osmosensory signaling pathway / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / pattern recognition receptor signaling pathway / microtubule organizing center / 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 / negative regulation of acute inflammatory response / signaling adaptor activity / positive regulation of interleukin-1 beta production / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / response to organic cyclic compound / ADP binding / positive regulation of inflammatory response / regulation of inflammatory response / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / response to ethanol / defense response to virus / sequence-specific DNA binding / defense response to Gram-positive bacterium / inflammatory response / Golgi membrane / innate immune response / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.55 Å | |||||||||||||||
Authors | Ohto U / Shimizu T | |||||||||||||||
Funding support | Japan, 4 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: Structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation. Authors: Umeharu Ohto / Yukie Kamitsukasa / Hanako Ishida / Zhikuan Zhang / Karin Murakami / Chie Hirama / Sakiko Maekawa / Toshiyuki Shimizu / Abstract: SignificanceThe nucleotide-binding oligomerization domain (NOD)-like receptor pyrin domain containing 3 (NLRP3) is a pattern recognition receptor that forms an inflammasome. The cryo-electron ...SignificanceThe nucleotide-binding oligomerization domain (NOD)-like receptor pyrin domain containing 3 (NLRP3) is a pattern recognition receptor that forms an inflammasome. The cryo-electron microscopy structure of the dodecameric form of full-length NLRP3 bound to the clinically relevant NLRP3-specific inhibitor MCC950 has established the structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation and the mechanism of action of the NLRP3 specific inhibitor. The inactive NLRP3 oligomer represents the NLRP3 resting state, capable of binding to membranes and is likely disrupted for its activation. Visualization of the inhibitor binding mode will enable optimization of the activity of NLRP3 inflammasome inhibitor drugs. | |||||||||||||||
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_32120.map.gz | 39.3 MB | EMDB map data format | |
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Header (meta data) | emd-32120-v30.xml emd-32120.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_32120.png | 144.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32120 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32120 | HTTPS FTP |
-Validation report
Summary document | emd_32120_validation.pdf.gz | 450.8 KB | Display | EMDB validaton report |
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Full document | emd_32120_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | emd_32120_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_32120_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32120 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32120 | HTTPS FTP |
-Related structure data
Related structure data | 7vtqMC 7vtpC 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_32120.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM map of mouse NLRP3 dodecamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 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 : Mouse NLRP3 (full-length) dodecamer
Entire | Name: Mouse NLRP3 (full-length) dodecamer |
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Components |
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-Supramolecule #1: Mouse NLRP3 (full-length) dodecamer
Supramolecule | Name: Mouse NLRP3 (full-length) dodecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: ExpiSf9 |
-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: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 121.415977 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: HHHHHHDYKD DDDKLEVLFQ GPEFMTSVRC KLAQYLEDLE DVDLKKFKMH LEDYPPEKGC IPVPRGQMEK ADHLDLATLM IDFNGEEKA WAMAVWIFAA INRRDLWEKA KKDQPEWNDT CTSHSSMVCQ EDSLEEEWMG LLGYLSRISI CKKKKDYCKM Y RRHVRSRF ...String: HHHHHHDYKD DDDKLEVLFQ GPEFMTSVRC KLAQYLEDLE DVDLKKFKMH LEDYPPEKGC IPVPRGQMEK ADHLDLATLM IDFNGEEKA WAMAVWIFAA INRRDLWEKA KKDQPEWNDT CTSHSSMVCQ EDSLEEEWMG LLGYLSRISI CKKKKDYCKM Y RRHVRSRF YSIKDRNARL GESVDLNSRY TQLQLVKEHP SKQEREHELL TIGRTKMRDS PMSSLKLELL FEPEDGHSEP VH TVVFQGA AGIGKTILAR KIMLDWALGK LFKDKFDYLF FIHCREVSLR TPRSLADLIV SCWPDPNPPV CKILRKPSRI LFL MDGFDE LQGAFDEHIG EVCTDWQKAV RGDILLSSLI RKKLLPKASL LITTRPVALE KLQHLLDHPR HVEILGFSEA KRKE YFFKY FSNELQAREA FRLIQENEVL FTMCFIPLVC WIVCTGLKQQ METGKSLAQT SKTTTAVYVF FLSSLLQSRG GIEEH LFSD YLQGLCSLAA DGIWNQKILF EECDLRKHGL QKTDVSAFLR MNVFQKEVDC ERFYSFSHMT FQEFFAAMYY LLEEEA EGE TVRKGPGGCS DLLNRDVKVL LENYGKFEKG YLIFVVRFLF GLVNQERTSY LEKKLSCKIS QQVRLELLKW IEVKAKA KK LQWQPSQLEL FYCLYEMQEE DFVQSAMDHF PKIEINLSTR MDHVVSSFCI KNCHRVKTLS LGFFHNSPKE EEEERRGG R PLDQVQCVFP DTHVACSSRL VNCCLTSSFC RGLFSSLSTN RSLTELDLSD NTLGDPGMRV LCEALQHPGC NIQRLWLGR CGLSHQCCFD ISSVLSSSQK LVELDLSDNA LGDFGIRLLC VGLKHLLCNL QKLWLVSCCL TSACCQDLAL VLSSNHSLTR LYIGENALG DSGVQVLCEK MKDPQCNLQK LGLVNSGLTS ICCSALTSVL KTNQNFTHLY LRSNALGDTG LRLLCEGLLH P DCKLQMLE LDNCSLTSHS CWNLSTILTH NHSLRKLNLG NNDLGDLCVV TLCEVLKQQG CLLQSLQLGE MYLNRETKRA LE ALQEEKP ELTIVFEISW |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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: 12 / Formula: 7YN |
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Molecular weight | Theoretical: 402.464 Da |
Chemical component information | ChemComp-7YN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 25 mM HEPES-NaOH (pH 7.5), 0.2 M NaCl, 1 mM MgCl2, 0.5 mM TCEP, 1.0 mM ADP, 0.05 mM MCC950 |
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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: 68.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73930 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |