+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14713 | |||||||||
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Title | Human NLRP3-deltaPYD hexamer | |||||||||
Map data | Map sharpened by DeepEMhancer from two halfmaps | |||||||||
Sample |
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Keywords | INFLAMMASOME / IMMUNITY / NOD-LIKE RECEPTOR / NACHT / LRR / PYD / 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 / negative regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / protein homooligomerization / Cytoprotection by HMOX1 / cellular response to virus / Metalloprotease DUBs / ADP binding / defense response / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Raisch T / Machtens DA / Bresch IB / Eberhage J / Prumbaum D / Reubold TF / Raunser S / Eschenburg S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the NEK7-independent NLRP3 inflammasome Authors: Raisch T / Machtens DA / Bresch IB / Eberhage J / Prumbaum D / Reubold TF / Raunser S / Eschenburg S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14713.map.gz | 327.5 MB | EMDB map data format | |
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Header (meta data) | emd-14713-v30.xml emd-14713.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_14713.png | 215.1 KB | ||
Filedesc metadata | emd-14713.cif.gz | 6.1 KB | ||
Others | emd_14713_additional_1.map.gz emd_14713_half_map_1.map.gz emd_14713_half_map_2.map.gz | 225.7 MB 189 MB 189 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14713 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14713 | HTTPS FTP |
-Validation report
Summary document | emd_14713_validation.pdf.gz | 858.2 KB | Display | EMDB validaton report |
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Full document | emd_14713_full_validation.pdf.gz | 857.8 KB | Display | |
Data in XML | emd_14713_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_14713_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14713 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14713 | HTTPS FTP |
-Related structure data
Related structure data | 7zguMC 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_14713.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map sharpened by DeepEMhancer from two halfmaps | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.68 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Additional map sharpened by Phenix
File | emd_14713_additional_1.map | ||||||||||||
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Annotation | Additional map sharpened by Phenix | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 from Sphire
File | emd_14713_half_map_1.map | ||||||||||||
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Annotation | Half map 1 from Sphire | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 from Sphire
File | emd_14713_half_map_2.map | ||||||||||||
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Annotation | Half map 2 from Sphire | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NLRP3 hexamer
Entire | Name: NLRP3 hexamer |
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Components |
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-Supramolecule #1: NLRP3 hexamer
Supramolecule | Name: NLRP3 hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 105.169375 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MRISICKMKK DYRKKYRKYV RSRFQCIEDR NARLGESVSL NKRYTRLRLI KEHRSQQERE QELLAIGKTK TCESPVSPIK MELLFDPDD EHSEPVHTVV FQGAAGIGKT ILARKMMLDW ASGTLYQDRF DYLFYIHCRE VSLVTQRSLG DLIMSCCPDP N PPIHKIVR ...String: MRISICKMKK DYRKKYRKYV RSRFQCIEDR NARLGESVSL NKRYTRLRLI KEHRSQQERE QELLAIGKTK TCESPVSPIK MELLFDPDD EHSEPVHTVV FQGAAGIGKT ILARKMMLDW ASGTLYQDRF DYLFYIHCRE VSLVTQRSLG DLIMSCCPDP N PPIHKIVR KPSRILFLMD GFDELQGAFD EHIGPLCTDW QKAERGDILL SSLIRKKLLP EASLLITTRP VALEKLQHLL DH PRHVEIL GFSEAKRKEY FFKYFSDEAQ ARAAFSLIQE NEVLFTMCFI PLVCWIVCTG LKQQMESGKS LAQTSKTTTA VYV FFLSSL LQPRGGSQEH GLCAHLWGLC SLAADGIWNQ KILFEESDLR NHGLQKADVS AFLRMNLFQK EVDCEKFYSF IHMT FQEFF AAMYYLLEEE KEGRTNVPGS RLKLPSRDVT VLLENYGKFE KGYLIFVVRF LFGLVNQERT SYLEKKLSCK ISQQI RLEL LKWIEVKAKA KKLQIQPSQL ELFYCLYEMQ EEDFVQRAMD YFPKIEINLS TRMDHMVSSF CIENCHRVES LSLGFL HNM PKEEEEEEKE GRHLDMVQCV LPSSSHAACS HGLVNSHLTS SFCRGLFSVL STSQSLTELD LSDNSLGDPG MRVLCET LQ HPGCNIRRLW LGRCGLSHEC CFDISLVLSS NQKLVELDLS DNALGDFGIR LLCVGLKHLL CNLKKLWLVS CCLTSACC Q DLASVLSTSH SLTRLYVGEN ALGDSGVAIL CEKAKNPQCN LQKLGLVNSG LTSVCCSALS SVLSTNQNLT HLYLRGNTL GDKGIKLLCE GLLHPDCKLQ VLELDNCNLT SHCCWDLSTL LTSSQSLRKL SLGNNDLGDL GVMMFCEVLK QQSCLLQNLG LSEMYFNYE TKSALETLQE EKPELTVVFE PSWGSGGDYK DDDDK UniProtKB: NACHT, LRR and PYD domains-containing protein 3 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / 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
Concentration | 0.075 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs-corrected microscope |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 99.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |