8YD7 | pdb_00008yd7

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

• PDB DOI: https://doi.org/10.2210/pdb8YD7/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2024-02-19 Released: 2024-05-15 
• Deposition Author(s): Lin, S.-C., Yang, C.-Y.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

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

• PubMed: 38710704 
• DOI: https://doi.org/10.1038/s41467-024-47990-2
• Primary Citation 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.
Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan.
Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan.
Institute for Quantitative Biomedicine, Rutgers University, Department of Biochemistry and Microbiology, Rutgers University, Piscataway, NJ, 08854, USA.
Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan. [e-mail].
Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan. [e-mail].
Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, 70101, Taiwan. [e-mail].
Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A5B4C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A9B1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 220.63 kDa 
• Atom Count: 13,822 
• Modeled Residue Count: 1,684 
• Deposited Residue Count: 1,865 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASP8 and FADD-like apoptosis regulator subunit p12	A [auth G], F [auth H], G [auth I], H [auth K]	181	Homo sapiens	Mutation(s): 1  Gene Names: CFLAR, CASH, CASP8AP1, CLARP, MRIT
UniProt & NIH Common Fund Data Resources
Find proteins for O15519 (Homo sapiens) Explore O15519  Go to UniProtKB:  O15519
PHAROS:  O15519 GTEx:  ENSG00000003402

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-8	B [auth D], C, D [auth B], E, J [auth A]	185	Homo sapiens	Mutation(s): 2  Gene Names: CASP8, MCH5 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAS-associated death domain protein	I [auth L]	216	Homo sapiens	Mutation(s): 1  Gene Names: FADD, MORT1, GIG3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13158 (Homo sapiens) Explore Q13158  Go to UniProtKB:  Q13158
PHAROS:  Q13158 GTEx:  ENSG00000168040

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SE	K [auth G]	SELENIUM ATOM Se SPVXKVOXSXTJOY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth G], F [auth H], G [auth I], H [auth K]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.936	α = 90
b = 150.057	β = 90
c = 175.703	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Lin, S.-C., Yang, C.-Y.

---

Funding Organization	Location	Grant Number
Other government	Taiwan	--

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary