8YD7

Structure of FADD/Caspase-8/cFLIP death effector domain assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Deciphering DED assembly mechanisms in FADD-procaspase-8-cFLIP complexes regulating apoptosis.

Yang, C.Y.Lien, C.I.Tseng, Y.C.Tu, Y.F.Kulczyk, A.W.Lu, Y.C.Wang, Y.T.Su, T.W.Hsu, L.C.Lo, Y.C.Lin, S.C.

(2024) Nat Commun 15: 3791-3791

  • DOI: https://doi.org/10.1038/s41467-024-47990-2
  • Primary Citation of Related Structures:  
    8YBX, 8YD7, 8YD8

  • PubMed Abstract: 

    Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling towards cell survival or apoptosis. Understanding their three-dimensional regulatory mechanism has been limited by the absence of atomic coordinates for their ternary DED complex. By employing X-ray crystallography and cryogenic electron microscopy (cryo-EM), we present the atomic coordinates of human FADD-procaspase-8-cFLIP complexes, revealing structural insights into these critical interactions. These structures illustrate how FADD and cFLIP orchestrate the assembly of caspase-8-containing complexes and offer mechanistic explanations for their role in promoting or inhibiting apoptotic and necroptotic signaling. A helical procaspase-8-cFLIP hetero-double layer in the complex appears to promote limited caspase-8 activation for cell survival. Our structure-guided mutagenesis supports the role of the triple-FADD complex in caspase-8 activation and in regulating receptor-interacting protein kinase 1 (RIPK1). These results propose a unified mechanism for DED assembly and procaspase-8 activation in the regulation of apoptotic and necroptotic signaling across various cellular pathways involved in development, innate immunity, and disease.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CASP8 and FADD-like apoptosis regulator subunit p12A [auth G],
F [auth H],
G [auth I],
H [auth K]
181Homo sapiensMutation(s): 1 
Gene Names: CFLARCASHCASP8AP1CLARPMRIT
UniProt & NIH Common Fund Data Resources
Find proteins for O15519 (Homo sapiens)
Explore O15519 
Go to UniProtKB:  O15519
PHAROS:  O15519
GTEx:  ENSG00000003402 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15519
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-8B [auth D],
C,
D [auth B],
E,
J [auth A]
185Homo sapiensMutation(s): 2 
Gene Names: CASP8MCH5
EC: 3.4.22.61
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
GTEx:  ENSG00000064012 
Entity Groups  
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UniProt GroupQ14790
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAS-associated death domain proteinI [auth L]216Homo sapiensMutation(s): 1 
Gene Names: FADDMORT1GIG3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13158 (Homo sapiens)
Explore Q13158 
Go to UniProtKB:  Q13158
PHAROS:  Q13158
GTEx:  ENSG00000168040 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13158
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SE
Query on SE

Download Ideal Coordinates CCD File 
K [auth G]SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth G],
F [auth H],
G [auth I],
H [auth K]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.936α = 90
b = 150.057β = 90
c = 175.703γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentTaiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release