+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5830 | |||||||||
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Title | Unified assembly mechanism of ASC-dependent inflammasomes | |||||||||
Map data | Reconstruction of PYD filament | |||||||||
Sample |
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Keywords | helical polymer / variable twist / apoptosis / death domain | |||||||||
Function / homology | Function and homology information Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / 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 / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / AIM2 inflammasome complex ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / 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 / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / AIM2 inflammasome complex / macropinocytosis / NLRP1 inflammasome complex / icosanoid biosynthetic process / interleukin-6 receptor binding / NLRP3 inflammasome complex assembly / canonical inflammasome complex / positive regulation of adaptive immune response / NLRP3 inflammasome complex / BMP receptor binding / osmosensory signaling pathway / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / positive regulation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / tropomyosin binding / positive regulation of actin filament polymerization / negative regulation of NF-kappaB transcription factor activity / positive regulation of activated T cell proliferation / pyroptosis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / The NLRP3 inflammasome / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / positive regulation of phagocytosis / negative regulation of canonical NF-kappaB signal transduction / positive regulation of chemokine production / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein stability / protein homooligomerization / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / azurophil granule lumen / positive regulation of T cell activation / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / defense response to virus / secretory granule lumen / cellular response to lipopolysaccharide / protease binding / defense response to Gram-negative bacterium / microtubule / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / Neutrophil degranulation / nucleolus / enzyme binding / endoplasmic reticulum / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Lu A / Magupalli VG / Ruan J / Yin Q / Atianand MK / Vos M / Schroder GF / Fitzgerald KA / Wu H / Egelman EH | |||||||||
Citation | Journal: Cell / Year: 2014 Title: Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Authors: Alvin Lu / Venkat Giri Magupalli / Jianbin Ruan / Qian Yin / Maninjay K Atianand / Matthijn R Vos / Gunnar F Schröder / Katherine A Fitzgerald / Hao Wu / Edward H Egelman / Abstract: Inflammasomes elicit host defense inside cells by activating caspase-1 for cytokine maturation and cell death. AIM2 and NLRP3 are representative sensor proteins in two major families of inflammasomes. ...Inflammasomes elicit host defense inside cells by activating caspase-1 for cytokine maturation and cell death. AIM2 and NLRP3 are representative sensor proteins in two major families of inflammasomes. The adaptor protein ASC bridges the sensor proteins and caspase-1 to form ternary inflammasome complexes, achieved through pyrin domain (PYD) interactions between sensors and ASC and through caspase activation and recruitment domain (CARD) interactions between ASC and caspase-1. We found that PYD and CARD both form filaments. Activated AIM2 and NLRP3 nucleate PYD filaments of ASC, which, in turn, cluster the CARD of ASC. ASC thus nucleates CARD filaments of caspase-1, leading to proximity-induced activation. Endogenous NLRP3 inflammasome is also filamentous. The cryoelectron microscopy structure of ASC(PYD) filament at near-atomic resolution provides a template for homo- and hetero-PYD/PYD associations, as confirmed by structure-guided mutagenesis. We propose that ASC-dependent inflammasomes in both families share a unified assembly mechanism that involves two successive steps of nucleation-induced polymerization. PAPERFLICK: | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5830.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-5830-v30.xml emd-5830.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | 400_5830.gif 80_5830.gif | 76.8 KB 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5830 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5830 | HTTPS FTP |
-Related structure data
Related structure data | 3j63MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5830.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of PYD filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PYD domain from ASC
Entire | Name: PYD domain from ASC |
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Components |
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-Supramolecule #1000: PYD domain from ASC
Supramolecule | Name: PYD domain from ASC / type: sample / ID: 1000 / Oligomeric state: helical polymer / Number unique components: 1 |
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-Macromolecule #1: Apoptosis-associated speck-like protein containing a CARD
Macromolecule | Name: Apoptosis-associated speck-like protein containing a CARD type: protein_or_peptide / ID: 1 / Name.synonym: pyrin domain, death domain / Oligomeric state: helical polymer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Grid | Details: over holes in lacey carbon grids, no support |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Dec 20, 2012 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 400 / Average electron dose: 20 e/Å2 / Details: Integrating mode used |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 13.95 Å Applied symmetry - Helical parameters - Δ&Phi: 52.9 ° Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider, IHRSR |
Details | IHRSR |