8YNK | pdb_00008ynk

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YNK

This is version 1.0 of the entry. See complete history

Literature

Reverse hierarchical DED assembly in the cFLIP-procaspase-8 and cFLIP-procaspase-8-FADD complexes.

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

(2024) Nat Commun 15: 8974-8974

  • DOI: https://doi.org/10.1038/s41467-024-53306-1
  • Primary Citation Related Structures: 
    8YM4, 8YM5, 8YM6, 8YNI, 8YNK, 8YNL, 8YNM, 8YNN

  • PubMed Abstract: 

    cFLIP, a master anti-apoptotic regulator, targets the FADD-induced DED complexes of procaspase-8 in death receptor and ripoptosome signaling pathways. Several tumor cells maintain relatively high levels of cFLIP in achieving their immortality. However, understanding the three-dimensional regulatory mechanism initiated or mediated by elevated levels of cFLIP has been limited by the absence of the atomic coordinates for cFLIP-induced DED complexes. Here we report the crystal plus cryo-EM structures to uncover an unconventional mechanism where cFLIP and procaspase-8 autonomously form a binary tandem DED complex, independent of FADD. This complex gains the ability to recruit FADD, thereby allosterically modulating cFLIP assembly and partially activating caspase-8 for RIPK1 cleavage. Our structure-guided mutagenesis experiments provide critical insights into these regulatory mechanisms, elucidating the resistance to apoptosis and necroptosis in achieving immortality. Finally, this research offers a unified model for the intricate bidirectional hierarchy-based processes using multiprotein helical assembly to govern cell fate decisions.


  • Organizational Affiliation
    • Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 269.97 kDa 
  • Atom Count: 11,564 
  • Modeled Residue Count: 1,409 
  • Deposited Residue Count: 2,342 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-8 subunit p10
A, B, C
479Homo sapiensMutation(s): 5 
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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14790
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CASP8 and FADD-like apoptosis regulator subunit p43D [auth H],
E [auth I],
F [auth J],
G [auth K],
H [auth G]
181Homo sapiensMutation(s): 0 
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARCV4.2

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: 2024-10-30
    Type: Initial release