+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2971 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure and assembly of the mouse ASC filament | |||||||||
Map data | Reconstruction of ASC-PYD filament | |||||||||
Sample |
| |||||||||
Keywords | ASC Apoptosis associated speck like protein containing a CARD / CARD caspase recruitment and activation domain / PYD PYRIN domain / PYHIN pyrin domain and hematopoietic expression / interferon inducibility / nuclear localization domain containing / NLR NOD like receptor / BIR Baculovirus IAP repeat domain | |||||||||
Function / homology | Function and homology information interleukin-1 beta production / CLEC7A/inflammasome pathway / positive regulation of chemokine production => GO:0032722 / Pyrin domain binding / myosin I binding / regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / peptidase activator activity involved in apoptotic process ...interleukin-1 beta production / CLEC7A/inflammasome pathway / positive regulation of chemokine production => GO:0032722 / Pyrin domain binding / myosin I binding / regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / peptidase activator activity involved in apoptotic process / myeloid dendritic cell activation / IkappaB kinase complex / AIM2 inflammasome complex / macropinocytosis / interleukin-6 receptor binding / NLRP1 inflammasome complex / positive regulation of adaptive immune response / NLRP3 inflammasome complex / BMP receptor binding / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / positive regulation of cysteine-type endopeptidase activity / activation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of NF-kappaB transcription factor activity / regulation of GTPase activity / positive regulation of actin filament polymerization / tropomyosin binding / positive regulation of activated T cell proliferation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of interleukin-10 production / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / Neutrophil degranulation / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / response to bacterium / positive regulation of DNA-binding transcription factor activity / regulation of protein stability / protein homooligomerization / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of T cell activation / regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / protease binding / cellular response to lipopolysaccharide / regulation of apoptotic process / defense response to virus / defense response to Gram-negative bacterium / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / inflammatory response / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / nucleolus / apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Sborgi L / Ravotti F / Dandey VP / Dick MS / Mazur A / Reckel S / Chami M / Scherer S / Bockmann A / Egelman EH ...Sborgi L / Ravotti F / Dandey VP / Dick MS / Mazur A / Reckel S / Chami M / Scherer S / Bockmann A / Egelman EH / Stahlberg H / Broz P / Meier BH / Hiller S | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy. Authors: Lorenzo Sborgi / Francesco Ravotti / Venkata P Dandey / Mathias S Dick / Adam Mazur / Sina Reckel / Mohamed Chami / Sebastian Scherer / Matthias Huber / Anja Böckmann / Edward H Egelman / ...Authors: Lorenzo Sborgi / Francesco Ravotti / Venkata P Dandey / Mathias S Dick / Adam Mazur / Sina Reckel / Mohamed Chami / Sebastian Scherer / Matthias Huber / Anja Böckmann / Edward H Egelman / Henning Stahlberg / Petr Broz / Beat H Meier / Sebastian Hiller / Abstract: Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous ...Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2971.map.gz | 6.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2971-v30.xml emd-2971.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_2971.jpg | 1.9 MB | ||
Filedesc structureFactors | emd_2971_sf.cif.gz | 684.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2971 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2971 | HTTPS FTP |
-Validation report
Summary document | emd_2971_validation.pdf.gz | 368 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2971_full_validation.pdf.gz | 367.6 KB | Display | |
Data in XML | emd_2971_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2971 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2971 | HTTPS FTP |
-Related structure data
Related structure data | 2n1fMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2971.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of ASC-PYD filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Mouse ASC-PYD filament
Entire | Name: Mouse ASC-PYD filament |
---|---|
Components |
|
-Supramolecule #1000: Mouse ASC-PYD filament
Supramolecule | Name: Mouse ASC-PYD filament / type: sample / ID: 1000 / Number unique components: 1 |
---|
-Macromolecule #1: mouse ASC filament
Macromolecule | Name: mouse ASC filament / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: pLysS / Recombinant plasmid: pET28a |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 / Details: 25mM Tris 300mM NaCl |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: vitrified by plunging into liquid nitrogen-cooled liquid ethane Method: The grids were blotted for 1 s before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Date | Oct 10, 2014 |
Image recording | Category: CCD / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 21138 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -12 / Tilt angle max: 12 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were aligned using IHRSR |
---|---|
Final reconstruction | Applied symmetry - Helical parameters - Δz: 14.2 Å Applied symmetry - Helical parameters - Δ&Phi: 53 ° Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: EMAN2, IHRSR, SPIDER |
CTF correction | Details: CTFFIND3 |