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- PDB-9ncq: Cryo-EM structure of Fas-FADD complex -

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Basic information

Entry
Database: PDB / ID: 9ncq
TitleCryo-EM structure of Fas-FADD complex
Components
  • FAS-associated death domain protein
  • Tumor necrosis factor receptor superfamily member 6
KeywordsIMMUNE SYSTEM / Fas / CD94 / FADD / Caspase / DISC / Apoptosis / Innate Immunity / helical assembly
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / Fas signaling pathway / cellular response to hyperoxia / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / Fas signaling pathway / cellular response to hyperoxia / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / activation-induced cell death of T cells / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / caspase binding / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / 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 / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / positive regulation of innate immune response / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / regulation of stress-activated MAPK cascade / positive regulation of reactive oxygen species biosynthetic process / positive regulation of activated T cell proliferation / T cell homeostasis / 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 / signaling adaptor activity / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to amino acid starvation / thymus development / positive regulation of apoptotic signaling pathway / positive regulation of interleukin-8 production / apoptotic signaling pathway / kidney development / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / Regulation of necroptotic cell death / positive regulation of T cell mediated cytotoxicity / kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / signaling receptor activity / cell body / protease binding / protein-containing complex assembly / regulation of apoptotic process / protein-macromolecule adaptor activity / defense response to virus / calmodulin binding / positive regulation of canonical NF-kappaB signal transduction / immune response / nuclear body / positive regulation of apoptotic process / membrane raft / innate immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / 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
Tumor necrosis factor receptor superfamily member 6 / FAS-associated death domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsFosuah, E. / Lin, Q. / Shen, Z. / Fu, T.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Assembly and activation of the death-inducing signaling complex.
Authors: Elizabeth Fosuah / Zhangfei Shen / Jiale Xie / Chen Wang / Qingpeng Lin / Tian-Min Fu /
Abstract: The death-inducing signaling complex (DISC), comprising Fas, Fas-associated death domain (FADD), and caspase-8, initiates extrinsic apoptosis. Using cryogenic electron microscopy (cryo-EM), we show ...The death-inducing signaling complex (DISC), comprising Fas, Fas-associated death domain (FADD), and caspase-8, initiates extrinsic apoptosis. Using cryogenic electron microscopy (cryo-EM), we show that Fas and FADD death domains (DDs) form an asymmetric 7:5 oligomer, which promotes FADD death effector domain (DED) filament formation. Structural analysis reveals that FADD DED filaments closely resemble caspase-8 tandem DED filaments, suggesting that FADD DED serves as a nucleation scaffold for caspase-8 assembly. These findings provide a mechanistic framework for how DISC assembly initiates apoptosis and amplifies signaling via higher-order oligomerization.
History
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 6
B: Tumor necrosis factor receptor superfamily member 6
E: Tumor necrosis factor receptor superfamily member 6
G: Tumor necrosis factor receptor superfamily member 6
C: Tumor necrosis factor receptor superfamily member 6
F: Tumor necrosis factor receptor superfamily member 6
D: Tumor necrosis factor receptor superfamily member 6
H: FAS-associated death domain protein
I: FAS-associated death domain protein
L: FAS-associated death domain protein
K: FAS-associated death domain protein
J: FAS-associated death domain protein


Theoretical massNumber of molelcules
Total (without water)133,77312
Polymers133,77312
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
Tumor necrosis factor receptor superfamily member 6 / Apo-1 antigen / Apoptosis-mediating surface antigen FAS / FASLG receptor


Mass: 10857.491 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAS, APT1, FAS1, TNFRSF6
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25445
#2: 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: 11554.015 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13158
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Fas-FADD DD complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
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

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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 643286 / Symmetry type: POINT
RefinementHighest resolution: 3.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027608
ELECTRON MICROSCOPYf_angle_d0.44210348
ELECTRON MICROSCOPYf_dihedral_angle_d3.471099
ELECTRON MICROSCOPYf_chiral_restr0.0351290
ELECTRON MICROSCOPYf_plane_restr0.0021348

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