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- EMDB-62847: FADD-DED filaments coordinate complex IIa assembly during TNF-ind... -

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Basic information

Entry
Database: EMDB / ID: EMD-62847
TitleFADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
Map data
Sample
  • Complex: FADD-DED filament
    • Complex: FADD-filament
      • Protein or peptide: FAS-associated death domain protein
KeywordsRNA recognition / RNA helicase / ATP hydrolysis / RLR signaling / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / caspase binding / 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 / positive regulation of adaptive immune response / positive regulation of macrophage differentiation / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / receptor serine/threonine kinase binding / negative regulation of necroptotic process / tumor necrosis factor receptor binding / positive regulation of type I interferon-mediated signaling pathway / positive regulation of innate immune response / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / T cell homeostasis / positive regulation of activated T cell proliferation / positive regulation of proteolysis / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / lymph node development / spleen development / behavioral response to cocaine / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / thymus development / positive regulation of interleukin-8 production / apoptotic signaling pathway / kidney development / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / positive regulation of T cell mediated cytotoxicity / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / cell body / protease binding / protein-macromolecule adaptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / innate immune response / apoptotic process / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
FAS-associated death domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTan YB / Luo D
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP26-2021-0001 Singapore
CitationJournal: To Be Published
Title: FADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
Authors: Tan YB / Luo D
History
DepositionDec 23, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62847.png

Downloads & links

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Map

FileDownload / File: emd_62847.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 360 pix.
= 272.52 Å		0.76 Å/pix.
x 360 pix.
= 272.52 Å		0.76 Å/pix.
x 360 pix.
= 272.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.757 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.085242905 - 0.22489415
Average (Standard dev.)0.0011351659 (±0.00840223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 272.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62847_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62847_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62847_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FADD-DED filament

EntireName: FADD-DED filament
Components
  • Complex: FADD-DED filament
    • Complex: FADD-filament
      • Protein or peptide: FAS-associated death domain protein

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Supramolecule #1: FADD-DED filament

SupramoleculeName: FADD-DED filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: FADD-DED filament formation during apoptosis
Molecular weightTheoretical: 0.42 kDa/nm

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Supramolecule #2: FADD-filament

SupramoleculeName: FADD-filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all / Details: FADD-filament
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: FAS-associated death domain protein

MacromoleculeName: FAS-associated death domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.104606 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDPFLVLLHS VSSSLSSSEL TELKFLCLGR VGKRKLERVQ SGLDLFSMLL EQNDLEPGHT ELLRELLASL RRHDLLRRVD DFEAGAAAG AA

UniProtKB: FAS-associated death domain protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.175 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
150.0 mMNaClsodium chloride

Details: 25mM HEPES, 150mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
Details: grid was precoated with graphene monolayer and glow discharged.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample forms filament.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 6256 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 13.97 Å
Applied symmetry - Helical parameters - Δ&Phi: 49.53 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: helical refinement / Details: helical refinement / Number images used: 300
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionSoftware: (Name: Topaz, cryoSPARC) / Details: topaz train/extract
Startup modelType of model: INSILICO MODEL / In silico model: ModelAngelo generated backbone PDB model.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: helical refinement / Details: helical refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9l5w:
FADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis

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