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- PDB-1a1z: FADD DEATH EFFECTOR DOMAIN, F25G MUTANT, NMR MINIMIZED AVERAGE ST... -

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Basic information

Entry
Database: PDB / ID: 1a1z
TitleFADD DEATH EFFECTOR DOMAIN, F25G MUTANT, NMR MINIMIZED AVERAGE STRUCTURE
ComponentsFADD PROTEIN
KeywordsAPOPTOSIS / DEATH EFFECTOR DOMAIN
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 / caspase binding / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / positive regulation of adaptive immune response / Caspase activation via Death Receptors in the presence of ligand / positive regulation of macrophage differentiation / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / negative regulation of necroptotic process / receptor serine/threonine kinase binding / positive regulation of type I interferon-mediated signaling pathway / tumor necrosis factor receptor binding / death receptor binding / positive regulation of innate immune response / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / motor neuron apoptotic process / RIPK1-mediated regulated necrosis / positive regulation of activated T cell proliferation / T cell homeostasis / positive regulation of proteolysis / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway via death domain receptors / lymph node development / behavioral response to cocaine / spleen development / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / thymus development / positive regulation of interleukin-8 production / kidney development / apoptotic signaling pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / positive regulation of T cell mediated cytotoxicity / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / cell body / protease binding / protein-macromolecule adaptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / 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 / 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 / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsEberstadt, M. / Huang, B. / Chen, Z. / Meadows, R.P. / Ng, C. / Fesik, S.W.
CitationJournal: Nature / Year: 1998
Title: NMR structure and mutagenesis of the FADD (Mort1) death-effector domain.
Authors: Eberstadt, M. / Huang, B. / Chen, Z. / Meadows, R.P. / Ng, S.C. / Zheng, L. / Lenardo, M.J. / Fesik, S.W.
History
DepositionDec 18, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)10,5451
Polymers10,5451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20TOTAL ENERGY
Representative

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Components

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


Mass: 10545.067 Da / Num. of mol.: 1 / Fragment: DEATH EFFECTOR DOMAIN / Mutation: F25G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: Q13158

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE MANUSCRIPT

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 100 mM / pH: 4 / Pressure: 1 atm / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker SEE MANUSCRIPTBrukerSEE MANUSCRIPT5001
Bruker SEE MANUSCRIPTBrukerSEE MANUSCRIPT6002
Bruker SEE MANUSCRIPTBrukerSEE MANUSCRIPT7503

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DREAMWALKER-WOOHOOstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 20 / Conformers submitted total number: 1

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