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- PDB-5xme: Solution structure of C-terminal domain of TRADD -

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Basic information

Entry
Database: PDB / ID: 5xme
TitleSolution structure of C-terminal domain of TRADD
ComponentsTumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsAPOPTOSIS / TRADD / death domain
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex ...tumor necrosis factor receptor superfamily complex / death domain binding / Defective RIPK1-mediated regulated necrosis / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / tumor necrosis factor receptor binding / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / kinase binding / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / cytoskeleton / receptor complex / positive regulation of cell migration / positive regulation of apoptotic process / apoptotic process / protein-containing complex binding / signal transduction / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / 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 type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsLin, Z. / Zhang, N.
CitationJournal: Sci Rep / Year: 2017
Title: Structure of the C-terminal domain of TRADD reveals a novel fold in the death domain superfamily.
Authors: Zhang, N. / Yuan, W. / Fan, J.S. / Lin, Z.
History
DepositionMay 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor type 1-associated DEATH domain protein


Theoretical massNumber of molelcules
Total (without water)14,4291
Polymers14,4291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7190 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor necrosis factor receptor type 1-associated DEATH domain protein / TNFR1-associated DEATH domain protein / TNFRSF1A-associated via death domain


Mass: 14429.224 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 199-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRADD / Production host: Escherichia coli (E. coli) / References: UniProt: Q15628

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
171isotropic14D 13C, 15N-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 0.6 mM U-99% 13C; U-99% 15N;U-98% 2H TRADD DD, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.6 mM / Component: TRADD DD / Isotopic labeling: U-99% 13C; U-99% 15N;U-98% 2H
Sample conditionsIonic strength units: Not defined / Label: sample_conditions_1 / pH: 5.0 / Pressure: 1 atm / Temperature: 301 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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