+Open data
-Basic information
Entry | Database: PDB / ID: 6npy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of NLRP3 bound to NEK7 | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / Inflammasome / Activator / Biological process Immunity / Inflammatory response / Innate immunity / Transcription / Transcription regulation Ligand / ATP binding / Nucleotide binding | |||||||||
Function / homology | Function and homology information NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / response to interferon-alpha / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation ...NEK6-subfamily protein kinase / regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / small molecule sensor activity / detection of biotic stimulus / eukaryotic translation initiation factor 2alpha kinase activity / cysteine-type endopeptidase activator activity / response to interferon-alpha / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / negative regulation of osteoblast proliferation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / NLRP3 inflammasome complex / regulation of hematopoietic progenitor cell differentiation / positive regulation of type 2 immune response / positive regulation of stress-activated MAPK cascade / cellular response to potassium ion / protein phosphatase regulator activity / Nuclear Pore Complex (NPC) Disassembly / osmosensory signaling pathway / peptidoglycan binding / SUMOylation of immune response proteins / regulation of hematopoietic stem cell proliferation / negative regulation of non-canonical NF-kappaB signal transduction / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / regulation of hematopoietic stem cell differentiation / microtubule organizing center / negative regulation of interleukin-1 beta production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / positive regulation of interleukin-4 production / pyroptotic inflammatory response / regulation of mitotic cell cycle / : / 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 / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / EML4 and NUDC in mitotic spindle formation / antiviral innate immune response / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / molecular function activator activity / non-specific protein-tyrosine kinase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of inflammatory response / non-membrane spanning protein tyrosine kinase activity / response to virus / positive regulation of non-canonical NF-kappaB signal transduction / PKR-mediated signaling / protein homooligomerization / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / cellular response to virus / Metalloprotease DUBs / ISG15 antiviral mechanism / ADP binding / defense response / spindle pole / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / Interferon alpha/beta signaling / kinase activity / 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 / defense response to virus / protein autophosphorylation / microtubule / positive regulation of MAPK cascade / molecular adaptor activity / non-specific serine/threonine protein kinase / negative regulation of translation / ribosome / protein kinase activity / translation / inflammatory response / protein phosphorylation / Golgi membrane / negative regulation of cell population proliferation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Sharif, H. / Wang, L. / Wang, W.L. / Wu, H. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nature / Year: 2019 Title: Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome. Authors: Humayun Sharif / Li Wang / Wei Li Wang / Venkat Giri Magupalli / Liudmila Andreeva / Qi Qiao / Arthur V Hauenstein / Zhaolong Wu / Gabriel Núñez / Youdong Mao / Hao Wu / Abstract: The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation ...The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6npy.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6npy.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 6npy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6npy_validation.pdf.gz | 968.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6npy_full_validation.pdf.gz | 977 KB | Display | |
Data in XML | 6npy_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 6npy_validation.cif.gz | 54.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/6npy ftp://data.pdbj.org/pub/pdb/validation_reports/np/6npy | HTTPS FTP |
-Related structure data
Related structure data | 0476MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 117890.984 Da / Num. of mol.: 1 / Mutation: D133I, R135C, K136A, K140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP3, C1orf7, CIAS1, NALP3, PYPAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96P20 |
---|---|
#2: Protein | Mass: 32015.150 Da / Num. of mol.: 1 / Mutation: L54R, V58K, P59T, K87A, A99V, S100C, E103T, D104G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2AK2, PKR, PRKR, NEK7 / Production host: Escherichia coli (E. coli) References: UniProt: P19525, UniProt: Q8TDX7, non-specific serine/threonine protein kinase |
#3: Chemical | ChemComp-ADP / |
Sequence details | The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total ...The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.1 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108771 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |