+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8300 | |||||||||
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Title | Cryo-EM structure of Casp-8 tDED filament (CASP target) | |||||||||
Map data | Casp-8 tDED filament | |||||||||
Sample |
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Function / homology | Function and homology information caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria ...caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / self proteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of necroptotic process / CLEC7A/inflammasome pathway / natural killer cell activation / regulation of tumor necrosis factor-mediated signaling pathway / activation of cysteine-type endopeptidase activity / death receptor binding / tumor necrosis factor receptor binding / cysteine-type endopeptidase activity involved in apoptotic process / TNFR1-induced proapoptotic signaling / execution phase of apoptosis / RIPK1-mediated regulated necrosis / regulation of innate immune response / B cell activation / pyroptosis / Apoptotic cleavage of cellular proteins / positive regulation of proteolysis / macrophage differentiation / protein maturation / extrinsic apoptotic signaling pathway via death domain receptors / cellular response to organic cyclic compound / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / cysteine-type peptidase activity / extrinsic apoptotic signaling pathway / regulation of cytokine production / negative regulation of canonical NF-kappaB signal transduction / T cell activation / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / response to estradiol / cell body / heart development / peptidase activity / scaffold protein binding / angiogenesis / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / response to lipopolysaccharide / cytoskeleton / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Fu TM / Li Y / Wu H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2016 Title: Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Authors: Tian-Min Fu / Yang Li / Alvin Lu / Zongli Li / Parimala R Vajjhala / Anthony C Cruz / Devendra B Srivastava / Frank DiMaio / Pawel A Penczek / Richard M Siegel / Katryn J Stacey / Edward H Egelman / Hao Wu / Abstract: Caspase-8 activation can be triggered by death receptor-mediated formation of the death-inducing signaling complex (DISC) and by the inflammasome adaptor ASC. Caspase-8 assembles with FADD at the ...Caspase-8 activation can be triggered by death receptor-mediated formation of the death-inducing signaling complex (DISC) and by the inflammasome adaptor ASC. Caspase-8 assembles with FADD at the DISC and with ASC at the inflammasome through its tandem death effector domain (tDED), which is regulated by the tDED-containing cellular inhibitor cFLIP and the viral inhibitor MC159. Here we present the caspase-8 tDED filament structure determined by cryoelectron microscopy. Extensive assembly interfaces not predicted by the previously proposed linear DED chain model were uncovered, and were further confirmed by structure-based mutagenesis in filament formation in vitro and Fas-induced apoptosis and ASC-mediated caspase-8 recruitment in cells. Structurally, the two DEDs in caspase-8 use quasi-equivalent contacts to enable assembly. Using the tDED filament structure as a template, structural analyses reveal the interaction surfaces between FADD and caspase-8 and the distinct mechanisms of regulation by cFLIP and MC159 through comingling and capping, respectively. | |||||||||
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_8300.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-8300-v30.xml emd-8300.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_8300.png | 126.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8300 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8300 | HTTPS FTP |
-Related structure data
Related structure data | 5l08MC 5jqeC 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_8300.map.gz / Format: CCP4 / Size: 19.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Casp-8 tDED filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.62 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 : Caspase-8
Entire | Name: Caspase-8Caspase 8 |
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Components |
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-Supramolecule #1: Caspase-8
Supramolecule | Name: Caspase-8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Caspase-8
Macromolecule | Name: Caspase-8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: caspase-8 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDFSRNLYDI GEQLDSEDL A SLKFLSLD YI PQRKQEP IKD ALMLFQ RLQEKRMLEE SNLS FLKEL LFRIN RLDL LITYLNTRKE EMEREL QTP GRAQISAYRV MLYQISE EV SRSELRSF K FLLQEEISK CKLDDDMNLL DIFIEMEKR V ILGEGKLD IL ...String: MDFSRNLYDI GEQLDSEDL A SLKFLSLD YI PQRKQEP IKD ALMLFQ RLQEKRMLEE SNLS FLKEL LFRIN RLDL LITYLNTRKE EMEREL QTP GRAQISAYRV MLYQISE EV SRSELRSF K FLLQEEISK CKLDDDMNLL DIFIEMEKR V ILGEGKLD IL KRVCAQI NKS LLKIIN DYEE FSKE UniProtKB: Caspase-8 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: OTHER / Details: cryogen not identified. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 31.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.1 Å Applied symmetry - Helical parameters - Δ&Phi: 99.4 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33969 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5l08: |