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- EMDB-8300: Cryo-EM structure of Casp-8 tDED filament (CASP target) -

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Basic information

Entry
Database: EMDB / ID: EMD-8300
TitleCryo-EM structure of Casp-8 tDED filament (CASP target)
Map dataCasp-8 tDED filament
Sample
  • Complex: Caspase-8
    • Protein or peptide: Caspase-8
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 / Apoptotic execution phase / ripoptosome / Defective RIPK1-mediated regulated necrosis / 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 / Apoptotic execution phase / ripoptosome / Defective RIPK1-mediated regulated necrosis / Activation, myristolyation of BID and translocation to mitochondria / Microbial modulation of RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / Caspase activation via Death Receptors in the presence of ligand / self proteolysis / positive regulation of macrophage differentiation / response to cobalt ion / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / CLEC7A/inflammasome pathway / death-inducing signaling complex / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / natural killer cell activation / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / response to anesthetic / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to tumor necrosis factor / B cell activation / positive regulation of proteolysis / macrophage differentiation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / Caspase-mediated cleavage of cytoskeletal proteins / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / regulation of cytokine production / proteolysis involved in protein catabolic process / T cell activation / protein maturation / positive regulation of interleukin-1 beta production / Regulation of NF-kappa B signaling / apoptotic signaling pathway / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein processing / Regulation of necroptotic cell death / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / lamellipodium / heart development / cell body / scaffold protein binding / response to ethanol / angiogenesis / response to lipopolysaccharide / mitochondrial outer membrane / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol
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 family 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)
Methodhelical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsFu TM / Li Y / Wu H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01-AI045937 United States
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 22, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5l08
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5l08
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8300.png

Downloads & links

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Map

FileDownload / File: emd_8300.map.gz / Format: CCP4 / Size: 19.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCasp-8 tDED filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.62 Å/pix.
x 200 pix.
= 124. Å		0.62 Å/pix.
x 160 pix.
= 99.2 Å		0.62 Å/pix.
x 160 pix.
= 99.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-104.109300000000005 - 66.495609999999999
Average (Standard dev.)-31.219836999999998 (±18.085826999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-99
Dimensions160160200
Spacing160160200
CellA: 99.2 Å / B: 99.2 Å / C: 124.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.620.620.62
M x/y/z160160200
origin x/y/z0.0000.0000.000
length x/y/z99.20099.200124.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS-80-80-99
NC/NR/NS160160200
D min/max/mean-104.10966.496-31.220

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Supplemental data

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Sample components

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Entire : Caspase-8

EntireName: Caspase-8
Components
  • Complex: Caspase-8
    • Protein or peptide: Caspase-8

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Supramolecule #1: Caspase-8

SupramoleculeName: Caspase-8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caspase-8

MacromoleculeName: Caspase-8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: caspase-8
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Component:
FormulaName
C4H12ClNO3Tris-HCl
NaClsodium chloride
VitrificationCryogen name: OTHER / Details: cryogen not identified.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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