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Basic information
| Entry | Database: PDB / ID: 8ym6 | ||||||
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| Title | Structure of Caspase-8/cFLIP death effector domain assembly | ||||||
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Keywords | APOPTOSIS / FADD / Caspase-8 / cFLIP / death effector domain | ||||||
| Function / homology | Function and homology informationnegative regulation of myoblast fusion / skeletal muscle atrophy / skeletal myofibril assembly / caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation ...negative regulation of myoblast fusion / skeletal muscle atrophy / skeletal myofibril assembly / caspase-8 / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / death effector domain binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / Apoptotic execution phase / Activation, myristolyation of BID and translocation to mitochondria / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / regulation of necroptotic process / positive regulation of extracellular matrix organization / self proteolysis / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / negative regulation of hepatocyte apoptotic process / positive regulation of glomerular mesangial cell proliferation / response to cobalt ion / skeletal muscle tissue regeneration / positive regulation of hepatocyte proliferation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / CLEC7A/inflammasome pathway / death-inducing signaling complex / negative regulation of necroptotic process / regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / natural killer cell activation / TNFR1-induced proapoptotic signaling / negative regulation of cellular response to transforming growth factor beta stimulus / negative regulation of cardiac muscle cell apoptotic process / RIPK1-mediated regulated necrosis / response to anesthetic / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / response to testosterone / response to tumor necrosis factor / B cell activation / positive regulation of proteolysis / macrophage differentiation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / Caspase-mediated cleavage of cytoskeletal proteins / cellular response to dexamethasone stimulus / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / cellular response to nitric oxide / regulation of cytokine production / proteolysis involved in protein catabolic process / cellular response to epidermal growth factor stimulus / T cell activation / protein maturation / positive regulation of interleukin-1 beta production / negative regulation of extrinsic apoptotic signaling pathway / Regulation of NF-kappa B signaling / apoptotic signaling pathway / enzyme activator activity / cellular response to estradiol stimulus / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / positive regulation of neuron projection development / protein processing / Regulation of necroptotic cell death / cellular response to insulin stimulus / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / lamellipodium / heart development / cell body / protease binding / scaffold protein binding / response to ethanol / angiogenesis / response to lipopolysaccharide / cellular response to hypoxia / mitochondrial outer membrane / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / positive regulation of apoptotic process Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Lin, S.-C. / Yang, C.-Y. | ||||||
| Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2024Title: Reverse hierarchical DED assembly in the cFLIP-procaspase-8 and cFLIP-procaspase-8-FADD complexes. Authors: Chao-Yu Yang / Yi-Chun Tseng / Yi-Fan Tu / Bai-Jiun Kuo / Li-Chung Hsu / Chia-I Lien / You-Sheng Lin / Yin-Ting Wang / Yen-Chen Lu / Tsung-Wei Su / Yu-Chih Lo / Su-Chang Lin / ![]() 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 ...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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Download
| PDBx/mmCIF format | 8ym6.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb8ym6.ent.gz | 812.3 KB | Display | PDB format |
| PDBx/mmJSON format | 8ym6.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8ym6_validation.pdf.gz | 505.2 KB | Display | wwPDB validaton report |
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| Full document | 8ym6_full_validation.pdf.gz | 520.2 KB | Display | |
| Data in XML | 8ym6_validation.xml.gz | 80.2 KB | Display | |
| Data in CIF | 8ym6_validation.cif.gz | 102.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/8ym6 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/8ym6 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8ym4C ![]() 8ym5C ![]() 8yniC ![]() 8ynkC ![]() 8ynlC ![]() 8ynmC ![]() 8ynnC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
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About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
Taiwan, 1items
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