+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40811 | |||||||||
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Title | Cryo-EM structure of NLRP3 open octamer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Activated NLRP3 / Cryo-EM / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response ...small molecule sensor activity / detection of biotic stimulus / cysteine-type endopeptidase activator activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / positive regulation of type 2 immune response / osmosensory signaling pathway / peptidoglycan binding / negative regulation of non-canonical NF-kappaB signal transduction / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / microtubule organizing center / negative regulation of interleukin-1 beta production / positive regulation of interleukin-4 production / pyroptotic inflammatory response / negative regulation of acute inflammatory response / The NLRP3 inflammasome / protein maturation / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / molecular condensate scaffold 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 / Cytoprotection by HMOX1 / cellular response to virus / Metalloprotease DUBs / ADP binding / defense response / negative regulation of inflammatory response / positive regulation of inflammatory response / 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 / protein-macromolecule adaptor activity / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.39 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_40811.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-40811-v30.xml emd-40811.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_40811.png | 106.1 KB | ||
Filedesc metadata | emd-40811.cif.gz | 5.7 KB | ||
Others | emd_40811_additional_1.map.gz emd_40811_half_map_1.map.gz emd_40811_half_map_2.map.gz | 61.7 MB 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40811 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40811 | HTTPS FTP |
-Related structure data
Related structure data | 8swfMC 8swkC 8sxnC 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_40811.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_40811_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40811_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40811_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NLRP3 open octamer complex
Entire | Name: NLRP3 open octamer complex |
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Components |
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-Supramolecule #1: NLRP3 open octamer complex
Supramolecule | Name: NLRP3 open octamer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 8 / 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: 103.675742 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: AEYCKMKKDY RKKYRKYVRS RFQCIEDRNA RLGESVSLNK RYTRLRLIKE HRSQQEREQE LLAIGKTKTC ESPVSPIKME LLFDPDDEH SEPVHTVVFQ GAAGIGKTIL ARKMMLDWAS GTLYQDRFDY LFYIHCREVS LVTQRSLGDL IMSCCPDPNP P IHKIVRKP ...String: AEYCKMKKDY 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: 1.2 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: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 466664 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |