+Open data
-Basic information
Entry | Database: PDB / ID: 7lfh | ||||||||||||
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Title | Cryo-EM structure of NLRP3 double-ring cage, 6-fold (12-mer) | ||||||||||||
Components | NACHT, LRR and PYD domains-containing protein 3 | ||||||||||||
Keywords | IMMUNE SYSTEM / NLRP3 / NEK7 / nucleotid-binding / ATP-binding / inflammasome / immunity / innate immunity / NACHT / LRR / PYD | ||||||||||||
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 / NLRP3 inflammasome complex / positive regulation of type 2 immune response / leukocyte migration involved in inflammatory response / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / osmosensory signaling pathway / cellular response to peptidoglycan / negative regulation of non-canonical NF-kappaB signal transduction / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / microtubule organizing center / positive regulation of interleukin-4 production / pyroptotic inflammatory response / 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Andreeva, L. / Rawson, S. / Wu, H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell / Year: 2021 Title: NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation. Authors: Liudmila Andreeva / Liron David / Shaun Rawson / Chen Shen / Teerithveen Pasricha / Pablo Pelegrin / Hao Wu / Abstract: The NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important ...The NACHT-, leucine-rich-repeat- (LRR), and pyrin domain-containing protein 3 (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important clinical target against chronic inflammation. Here, we report that an endogenous, stimulus-responsive form of full-length mouse NLRP3 is a 12- to 16-mer double-ring cage held together by LRR-LRR interactions with the pyrin domains shielded within the assembly to avoid premature activation. Surprisingly, this NLRP3 form is predominantly membrane localized, which is consistent with previously noted localization of NLRP3 at various membrane organelles. Structure-guided mutagenesis reveals that trans-Golgi network dispersion into vesicles, an early event observed for many NLRP3-activating stimuli, requires the double-ring cages of NLRP3. Double-ring-defective NLRP3 mutants abolish inflammasome punctum formation, caspase-1 processing, and cell death. Thus, our data uncover a physiological NLRP3 oligomer on the membrane that is poised to sense diverse signals to induce inflammasome activation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lfh.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lfh.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 7lfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lfh ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lfh | HTTPS FTP |
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-Related structure data
Related structure data | 23302MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 118802.219 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrp3, Cias1, Mmig1, Nalp3, Pypaf1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8R4B8 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: NLRP3 double-ring cage, 6-fold (12-mer) / Type: COMPLEX / Details: NLRP3 oligomer / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.42 MDa / Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293T |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: -2400 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.51 sec. / Electron dose: 53.225 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6800 Details: Images were collected as movies with 50 frames, each recorded at multiple defocus values from -0.8 to -2.4 um and with multiple exposures per stage shift (5x4) introduced with image shift. |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122941 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6NPY Pdb chain-ID: A / Accession code: 6NPY / Pdb chain residue range: 131-1036 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
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