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- PDB-2gf5: Structure of intact FADD (MORT1) -

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Basic information

Entry
Database: PDB / ID: 2gf5
TitleStructure of intact FADD (MORT1)
ComponentsFADD protein
KeywordsAPOPTOSIS / Death domain / death effector domain / death-inducing signaling complex
Function / homology
Function and homology information


positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis ...positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / negative regulation of activation-induced cell death of T cells / death effector domain binding / tumor necrosis factor receptor superfamily binding / FasL/ CD95L signaling / TRAIL signaling / CD95 death-inducing signaling complex / death-inducing signaling complex assembly / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRAIL-activated apoptotic signaling pathway / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / caspase binding / 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 / necroptotic signaling pathway / positive regulation of macrophage differentiation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / activation of cysteine-type endopeptidase activity / death-inducing signaling complex / receptor serine/threonine kinase binding / negative regulation of necroptotic process / positive regulation of innate immune response / tumor necrosis factor receptor binding / positive regulation of type I interferon-mediated signaling pathway / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / motor neuron apoptotic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / T cell homeostasis / positive regulation of activated T cell proliferation / positive regulation of proteolysis / positive regulation of execution phase of apoptosis / behavioral response to cocaine / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / spleen development / extrinsic apoptotic signaling pathway / thymus development / kidney development / apoptotic signaling pathway / positive regulation of interleukin-8 production / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cellular response to mechanical stimulus / cytoplasmic side of plasma membrane / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / protein-macromolecule adaptor activity / T cell differentiation in thymus / cell body / protease binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / innate immune response / protein-containing complex binding / apoptotic process / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). ...FADD / : / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FAS-associated death domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCarrington, P.E. / Sandu, C. / Wei, Y. / Hill, J.M. / Morisawa, G. / Huang, T. / Gavathiotis, E. / Wei, Y. / Werner, M.H.
CitationJournal: Mol.Cell / Year: 2006
Title: The Structure of FADD and Its Mode of Interaction with Procaspase-8
Authors: Carrington, P.E. / Sandu, C. / Wei, Y. / Hill, J.M. / Morisawa, G. / Huang, T. / Gavathiotis, E. / Wei, Y. / Werner, M.H.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FADD protein


Theoretical massNumber of molelcules
Total (without water)21,5411
Polymers21,5411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 10025 structures for lowest energy
RepresentativeModel #1

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Components

#1: Protein FADD protein / FAS-associating death domain-containing protein / Mediator of receptor induced toxicity


Mass: 21541.430 Da / Num. of mol.: 1 / Mutation: F25Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FADD, MORT1 / Plasmid: pQE50 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13158

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited NOESY
12113C-edited NOESY
131CBCA(CO)NH
141HNCA
151C(CO)NH
161H(CCO)NH
171(H)CCH-TOCSY

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Sample preparation

DetailsContents: 200mM phosphate buffer, 95% H2O 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 200mM phosphate / pH: 7 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.12.2Brunger et al.refinement
X-PLOR2.12.2Brunger et al.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement
NMR ensembleConformer selection criteria: 25 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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