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- PDB-3oq9: Structure of the FAS/FADD death domain assembly -

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Basic information

Entry
Database: PDB / ID: 3oq9
TitleStructure of the FAS/FADD death domain assembly
Components
  • Protein FADD
  • Tumor necrosis factor receptor superfamily member 6
KeywordsAPOPTOSIS / DISC / FAS / FADD
Function / homology
Function and homology information


FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / regulation of myeloid cell differentiation / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of B cell activation / negative regulation of activation-induced cell death of T cells / regulation of B cell differentiation ...FasL/ CD95L signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / regulation of myeloid cell differentiation / positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of B cell activation / negative regulation of activation-induced cell death of T cells / regulation of B cell differentiation / B cell mediated immunity / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / lymphocyte apoptotic process / TRAIL signaling / CD95 death-inducing signaling complex / activation-induced cell death of T cells / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / caspase binding / 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 hematopoietic progenitor cell differentiation / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / negative thymic T cell selection / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / receptor serine/threonine kinase binding / negative regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / positive regulation of innate immune response / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / regulation of T cell differentiation / RIPK1-mediated regulated necrosis / cellular response to lithium ion / hepatocyte apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of activated T cell proliferation / T cell homeostasis / positive regulation of proteolysis / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / lymph node development / behavioral response to cocaine / spleen development / extrinsic apoptotic signaling pathway / signaling adaptor activity / extrinsic apoptotic signaling pathway in absence of ligand / response to glucocorticoid / thymus development / positive regulation of interleukin-8 production / apoptotic signaling pathway / kidney development / positive regulation of protein-containing complex assembly / Regulation of TNFR1 signaling / cellular response to mechanical stimulus / circadian rhythm / Regulation of necroptotic cell death / positive regulation of T cell mediated cytotoxicity / response to toxic substance / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / T cell differentiation in thymus / cell body / protease binding / neuron apoptotic process / protein-macromolecule adaptor activity / defense response to virus / gene expression / calmodulin binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / membrane raft / innate immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 6 / FAS-associated death domain protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.8 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: 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
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 6
B: Tumor necrosis factor receptor superfamily member 6
C: Tumor necrosis factor receptor superfamily member 6
D: Tumor necrosis factor receptor superfamily member 6
E: Tumor necrosis factor receptor superfamily member 6
H: Protein FADD
I: Protein FADD
J: Protein FADD
K: Protein FADD
L: Protein FADD


Theoretical massNumber of molelcules
Total (without water)109,23910
Polymers109,23910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.204, 144.447, 131.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Tumor necrosis factor receptor superfamily member 6 / FASLG receptor / Apoptosis-mediating surface antigen FAS / Apo-1 antigen


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
Protein FADD / FAS-associated death domain protein / FAS-associating death domain-containing protein / Mediator of ...FAS-associated death domain protein / FAS-associating death domain-containing protein / Mediator of receptor induced toxicity / Growth-inhibiting gene 3 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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 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

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorDetector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
6.8-7.042.70.4621580.78369.3
7.04-7.323.20.2731890.80187.9
7.32-7.664.30.2812300.96997
7.66-8.065.20.1792231.05297.4
8.06-8.565.50.1232241.18997
8.56-9.225.70.1122221.38495.7
9.22-10.145.80.0782251.70894.9
10.14-11.595.50.062252.13997
11.59-14.545.30.0532312.34894.7
14.54-504.40.0452483.02793.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.091 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.52 Å49.36 Å
Translation6.52 Å49.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.8→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3542 96 4.2 %random
Rwork0.3434 ---
obs-1941 85.6 %-
Solvent computationBsol: 383.707 Å2
Displacement parametersBiso max: 452.47 Å2 / Biso mean: 452.47 Å2 / Biso min: 452.47 Å2
Baniso -1Baniso -2Baniso -3
1--86.524 Å20 Å20 Å2
2--102.559 Å20 Å2
3----16.036 Å2
Refinement stepCycle: LAST / Resolution: 6.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7255 0 0 0 7255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d1.722
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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