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- PDB-1ich: SOLUTION STRUCTURE OF THE TUMOR NECROSIS FACTOR RECEPTOR-1 DEATH ... -

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Basic information

Entry
Database: PDB / ID: 1ich
TitleSOLUTION STRUCTURE OF THE TUMOR NECROSIS FACTOR RECEPTOR-1 DEATH DOMAIN
ComponentsTUMOR NECROSIS FACTOR RECEPTOR-1TNF receptor superfamily
KeywordsAPOPTOSIS / death domain
Function / homology
Function and homology information


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region ...Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, death domain / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / 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
Tumor necrosis factor receptor superfamily member 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, Simulated annealing, molecular dynamics
AuthorsSukits, S.F. / Lin, L.-L. / Malakian, K. / Powers, R. / Xu, G.-Y.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of the tumor necrosis factor receptor-1 death domain.
Authors: Sukits, S.F. / Lin, L.L. / Hsu, S. / Malakian, K. / Powers, R. / Xu, G.Y.
History
DepositionApr 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR RECEPTOR-1


Theoretical massNumber of molelcules
Total (without water)12,8081
Polymers12,8081
Non-polymers00
Water0
1


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

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Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR-1 / TNF receptor superfamily / TNF-1


Mass: 12807.777 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN / Mutation: R347K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSET(T7) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE) PLYS / References: UniProt: P19438

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1314D 13C-separated NOESY
NMR detailsText: The structure was determinined using 3D triple-resonance experiments with the enhanced-sensitivity pulse field gradient approach.

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Sample preparation

DetailsContents: 1 mM sample / Solvent system: 10 mM Sodium acetate at pH 4.0, 10 mM DTT
Sample conditionsIonic strength: 10 mM / pH: 4.0 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR9.8Badger, J., Kumar, R.A., Yip, P.structure solution
NMRPipe1.8, 2000Delaglio, F.processing
PIPP4.2.2, 1998Garrett, D.data analysis
X-PLOR9.8Badger, J., Kumar, R.A., Yip, P.refinement
RefinementMethod: Distance geometry, Simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures were based on a total of 1167 distance constraints from NOE and H-Bond, 117 dihedral angle constraints from 3D HNHA and TALOS program and 81 pairs of CA/CB chemical shift contraints.
NMR ensembleConformers submitted total number: 1

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