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- PDB-5l08: Cryo-EM structure of Casp-8 tDED filament -

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Basic information

Entry
Database: PDB / ID: 5l08
TitleCryo-EM structure of Casp-8 tDED filament
ComponentsCaspase-8
KeywordsAPOPTOSIS / Casp-8 / filament / DED / Death domain
Function / homology
Function and homology information


caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway ...caspase-8 / death effector domain binding / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / Defective RIPK1-mediated regulated necrosis / Apoptotic execution phase / TRAIL-activated apoptotic signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / 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 / self proteolysis / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / activation of cysteine-type endopeptidase activity / : / death-inducing signaling complex / CLEC7A/inflammasome pathway / negative regulation of necroptotic process / natural killer cell activation / tumor necrosis factor receptor binding / regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / : / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / execution phase of apoptosis / pyroptotic inflammatory response / regulation of innate immune response / Apoptotic cleavage of cellular proteins / positive regulation of proteolysis / B cell activation / cellular response to organic cyclic compound / protein maturation / macrophage differentiation / extrinsic apoptotic signaling pathway via death domain receptors / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / extrinsic apoptotic signaling pathway / regulation of cytokine production / T cell activation / positive regulation of interleukin-1 beta production / apoptotic signaling pathway / proteolysis involved in protein catabolic process / Regulation of NF-kappa B signaling / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / lamellipodium / response to estradiol / heart development / peptidase activity / cell body / scaffold protein binding / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / cytoskeleton / positive regulation of cell migration / positive regulation of apoptotic process / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / protein-containing complex binding / apoptotic process / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Caspase-8 / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...Caspase-8 / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsFu, T.M. / Li, Y. / Lu, A. / Wu, H.
CitationJournal: 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
DepositionJul 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Refinement description
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Caspase-8
B: Caspase-8
C: Caspase-8
D: Caspase-8
E: Caspase-8
F: Caspase-8
G: Caspase-8
H: Caspase-8
I: Caspase-8


Theoretical massNumber of molelcules
Total (without water)198,0049
Polymers198,0049
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18220 Å2
ΔGint4 kcal/mol
Surface area77480 Å2
SymmetryHelical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 27.1 Å / Rotation per n subunits: 99.4 °)

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Components

#1: Protein
Caspase-8 / CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3- ...CASP-8 / Apoptotic cysteine protease / Apoptotic protease Mch-5 / CAP4 / FADD-homologous ICE/ced-3-like protease / FADD-like ICE / FLICE / ICE-like apoptotic protease 5 / MORT1-associated ced-3 homolog / MACH


Mass: 22000.486 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8, MCH5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14790, caspase-8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Casp-8 tDED filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28a
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 31 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 99.4 ° / Axial rise/subunit: 27.1 Å / Axial symmetry: C3
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 33969 / Symmetry type: HELICAL

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