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- PDB-1e3y: Death domain from human FADD/MORT1 -

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Basic information

Entry
Database: PDB / ID: 1e3y
TitleDeath domain from human FADD/MORT1
ComponentsFADD PROTEIN
KeywordsAPOPTOSIS / DEATH DOMAIN / ADAPTER MOLECULE / FAS RECEPTOR DEATH INDUCING SIGNALLING 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 / FasL/ CD95L signaling / tumor necrosis factor receptor superfamily binding / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / TRAIL-activated apoptotic signaling pathway / death-inducing signaling complex assembly ...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 / FasL/ CD95L signaling / tumor necrosis factor receptor superfamily binding / TRAIL signaling / CD95 death-inducing signaling complex / ripoptosome / TRAIL-activated apoptotic signaling pathway / death-inducing signaling complex assembly / Defective RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / 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 / positive regulation of macrophage differentiation / necroptotic signaling pathway / caspase binding / 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 / 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 / RIPK1-mediated regulated necrosis / positive regulation of activated T cell proliferation / positive regulation of execution phase of apoptosis / T cell homeostasis / positive regulation of proteolysis / behavioral response to cocaine / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / signaling adaptor activity / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / thymus development / kidney development / positive regulation of interleukin-8 production / apoptotic signaling pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / cellular response to mechanical stimulus / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell body / T cell differentiation in thymus / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / protease binding / molecular adaptor activity / positive regulation of apoptotic process / innate immune response / apoptotic process / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm / cytosol
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 FROM RANDOM CHAIN STARTING CONFORMERS
Model type detailsMINIMIZED AVERAGE
AuthorsDriscoll, P.C. / Berglund, H. / Olerenshaw, D. / McDonald, N.Q.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The Three-Dimensional Solution Structure and Dynamic Properties of the Human Fadd Death Domain
Authors: Berglund, H. / Olerenshaw, D. / Sankar, A. / Federwisch, M. / Mcdonald, N.Q. / Driscoll, P.C.
History
DepositionJun 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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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)11,8701
Polymers11,8701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100LEAST RESTRAINT VIOLATION AND GOOD NON-BONDED CONTACTS
Representative

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Components

#1: Protein FADD PROTEIN / FAS-ASSOCIATING DEATH DOMAIN-CONTAINING PROTEIN


Mass: 11870.372 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN RESIDUES 93-192 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: PCR CLONING INTO N-TERMINAL 6*HIS TAG THROMBIN-CLEAVABLE FUSION PROTEIN
Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13158
Compound detailsCHIAN A EXTRA GLY-SER-HIS-MET- AT N-TERMINUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111VARIOUS DOUBLE
121TRIPLE RESONANCES EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED FADD-DD. FULL DETAILS ARE GIVEN IN BERGLUND ET AL., J. MOL. BIOL. (2000), IN PRESS

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Sample preparation

Sample conditionsIonic strength: 50 MM PHOSPHATE BUFFER, 150MM NACL / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NMRPipestructure solution
ANSIGstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING FROM RANDOM CHAIN STARTING CONFORMERS
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND GOOD NON-BONDED CONTACTS
Conformers calculated total number: 100 / Conformers submitted total number: 1

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