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- PDB-2ib1: Solution structure of p45 Death Domain -

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Basic information

Entry
Database: PDB / ID: 2ib1
TitleSolution structure of p45 Death Domain
ComponentsDeath domain containing membrane protein NRADD
KeywordsAPOPTOSIS / p45 / death domain / p75 / Nogo / FADD
Function / homology
Function and homology information


death receptor activity / neuron projection membrane / cell body membrane / neurotrophin p75 receptor binding / nerve growth factor binding / nuclear envelope lumen / Rho protein signal transduction / coreceptor activity / lamellipodium / apoptotic process ...death receptor activity / neuron projection membrane / cell body membrane / neurotrophin p75 receptor binding / nerve growth factor binding / nuclear envelope lumen / Rho protein signal transduction / coreceptor activity / lamellipodium / apoptotic process / cell surface / membrane / nucleus / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane 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
Death domain-containing membrane protein NRADD
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsVilar, M. / Sung, T.C. / Lee, K.F. / Riek, R.
CitationJournal: To be Published
Title: Solution Structure of p45 death domain
Authors: Vilar, M. / Sung, T.C. / Lee, K.F. / Riek, R.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 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: Death domain containing membrane protein NRADD


Theoretical massNumber of molelcules
Total (without water)9,9751
Polymers9,9751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Death domain containing membrane protein NRADD / Neurotrophin receptor associated death domain


Mass: 9975.160 Da / Num. of mol.: 1 / Fragment: residues 138-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nradd / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8CJ26

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA-J
1213D 15N-separated NOESY
1313D 13C-separated NOESY

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Sample preparation

DetailsContents: 1-2 mM protein, PBS (Phosphate Buffer Saline) buffer, pH 7.5, 298 K
Solvent system: PBS (Phosphate Buffer Saline) buffer, pH 7.5, 298 K
Sample conditionsIonic strength: 137 mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntertstructure solution
CNSrefinement
XwinNMRcollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1319 restraints, 1053 are NOE-derived distance constraints, 266 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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