+Open data
-Basic information
Entry | Database: PDB / ID: 3oq9 | ||||||
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Title | Structure of the FAS/FADD death domain assembly | ||||||
Components |
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Keywords | APOPTOSIS / DISC / FAS / FADD | ||||||
Function / homology | Function and homology information FasL/ CD95L signaling / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / Fas signaling pathway / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / regulation of myeloid cell differentiation ...FasL/ CD95L signaling / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / Fas signaling pathway / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / regulation of myeloid cell differentiation / cellular response to hyperoxia / negative regulation of B cell activation / death effector domain binding / regulation of B cell differentiation / FasL/ CD95L signaling / B cell mediated immunity / negative regulation of Schwann cell migration / tumor necrosis factor receptor activity / lymphocyte apoptotic process / TRAIL signaling / CD95 death-inducing signaling complex / tumor necrosis factor receptor superfamily binding / death-inducing signaling complex assembly / ripoptosome / activation-induced cell death of T cells / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / regulation of hematopoietic progenitor cell differentiation / TLR3-mediated TICAM1-dependent programmed cell death / negative regulation of Schwann cell proliferation / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / negative thymic T cell selection / positive regulation of macrophage differentiation / caspase binding / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / apical dendrite / death-inducing signaling complex / negative regulation of necroptotic process / receptor serine/threonine kinase binding / activation of cysteine-type endopeptidase activity / positive regulation of innate immune response / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / motor neuron apoptotic process / TNFR1-induced proapoptotic signaling / regulation of T cell differentiation / RIPK1-mediated regulated necrosis / positive regulation of execution phase of apoptosis / regulation of stress-activated MAPK cascade / positive regulation of activated T cell proliferation / cellular response to lithium ion / hepatocyte apoptotic process / T cell homeostasis / behavioral response to cocaine / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / signaling adaptor activity / positive regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway / response to glucocorticoid / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / cellular response to amino acid starvation / thymus development / secretory granule / kidney development / positive regulation of interleukin-8 production / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / Regulation of TNFR1 signaling / sarcolemma / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / response to toxic substance / kinase binding / positive regulation of T cell mediated cytotoxicity / cellular response to mechanical stimulus / circadian rhythm / positive regulation of neuron apoptotic process / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / cell body / gene expression / regulation of cell population proliferation / neuron apoptotic process / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / protease binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.8 Å | ||||||
Authors | Kabaleeswaran, V. / Wu, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: The Fas-FADD death domain complex structure reveals the basis of DISC assembly and disease mutations. Authors: Wang, L. / Yang, J.K. / Kabaleeswaran, V. / Rice, A.J. / Cruz, A.C. / Park, A.Y. / Yin, Q. / Damko, E. / Jang, S.B. / Raunser, S. / Robinson, C.V. / Siegel, R.M. / Walz, T. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oq9.cif.gz | 161.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oq9.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 3oq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oq9 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oq9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10162.680 Da / Num. of mol.: 5 / Fragment: UNP residues 223-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fas, Apt1, Tnfrsf6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25446 #2: Protein | Mass: 11685.176 Da / Num. of mol.: 5 / Fragment: UNP residues 93-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1, GIG3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13158 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 100 mM MgCl2, 5 % glycerol and 6-10 % PEG4000, hanging drop, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Detector: CCD / Date: Apr 13, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 6.8→50 Å / Num. obs: 2175 / % possible obs: 92.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Χ2: 1.649 / Net I/σ(I): 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 45.091 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.8→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 383.707 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 452.47 Å2 / Biso mean: 452.47 Å2 / Biso min: 452.47 Å2
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Refinement step | Cycle: LAST / Resolution: 6.8→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param |