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- PDB-9l5w: FADD-DED filaments coordinate complex IIa assembly during TNF-ind... -

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Basic information

Entry
Database: PDB / ID: 9l5w
TitleFADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
ComponentsFAS-associated death domain protein
KeywordsIMMUNE SYSTEM / RNA recognition / RNA helicase / ATP hydrolysis / RLR signaling
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsTan, Y.B. / Luo, D.
Funding support Singapore, 1items
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, Y.B. / Luo, D.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAS-associated death domain protein
B: FAS-associated death domain protein
C: FAS-associated death domain protein
D: FAS-associated death domain protein
E: FAS-associated death domain protein
F: FAS-associated death domain protein
G: FAS-associated death domain protein
H: FAS-associated death domain protein
I: FAS-associated death domain protein
J: FAS-associated death domain protein
K: FAS-associated death domain protein
L: FAS-associated death domain protein
M: FAS-associated death domain protein
N: FAS-associated death domain protein
O: FAS-associated death domain protein
P: FAS-associated death domain protein
Q: FAS-associated death domain protein
R: FAS-associated death domain protein


Theoretical massNumber of molelcules
Total (without water)181,88318
Polymers181,88318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
FAS-associated death domain protein / FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of ...FAS-associating death domain-containing protein / Growth-inhibiting gene 3 protein / Mediator of receptor induced toxicity


Mass: 10104.606 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13158
Has protein modificationN

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1FADD-DED filamentCOMPLEXFADD-DED filament formation during apoptosisall0RECOMBINANT
2FADD-filamentCOMPLEXFADD-filamentall1RECOMBINANT
Molecular weightValue: 0.42 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 25mM HEPES, 150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.175 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample forms filament.
Specimen supportDetails: grid was precoated with graphene monolayer and glow discharged.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6256

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2cryoSPARCparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignmenthelical refinement
12cryoSPARCclassificationheterogenous refinement
13cryoSPARC3D reconstructionhelical refinement
14PHENIX1.20.1_4487:model refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 49.53 ° / Axial rise/subunit: 13.97 Å / Axial symmetry: C3
Particle selectionDetails: topaz train/extract
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 300 / Details: helical refinement / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311808
ELECTRON MICROSCOPYf_angle_d0.5615840
ELECTRON MICROSCOPYf_dihedral_angle_d3.4311584
ELECTRON MICROSCOPYf_chiral_restr0.041890
ELECTRON MICROSCOPYf_plane_restr0.0042016

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