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- PDB-2mjo: NMR structure of p75 transmembrane domain C257A mutant in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2mjo
TitleNMR structure of p75 transmembrane domain C257A mutant in DPC micelles
ComponentsTumor necrosis factor receptor superfamily member 16
KeywordsMEMBRANE PROTEIN / p75 / dimer / transmembrane / C257A mutation
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / death receptor activity / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / positive regulation of synaptic transmission, cholinergic / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / negative regulation of dendritic spine development / positive regulation of myelination / nerve development / clathrin-coated endocytic vesicle / nerve growth factor binding / neurotrophin TRKA receptor binding / positive regulation of neural precursor cell proliferation / regulation of reactive oxygen species metabolic process / negative regulation of mitochondrial depolarization / skin development / hair follicle morphogenesis / positive regulation of Rho protein signal transduction / neuronal cell body membrane / skeletal muscle cell differentiation / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / positive regulation of excitatory postsynaptic potential / Rho protein signal transduction / hair follicle development / fibroblast growth factor receptor signaling pathway / coreceptor activity / dendrite membrane / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / negative regulation of angiogenesis / positive regulation of synaptic transmission, glutamatergic / negative regulation of cell migration / central nervous system development / positive regulation of apoptotic signaling pathway / axon guidance / intracellular protein transport / circadian regulation of gene expression / neuromuscular junction / small GTPase binding / positive regulation of neuron projection development / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / positive regulation of fibroblast proliferation / cell-cell junction / presynapse / negative regulation of neuron projection development / glucose homeostasis / presynaptic membrane / nuclear envelope / cellular response to oxidative stress / amyloid-beta binding / growth cone / fibroblast proliferation / regulation of gene expression / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / dendritic spine / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / calmodulin binding / positive regulation of apoptotic process / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1780 / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1780 / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Death-like domain superfamily / Helix non-globular / Special
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsNadezhdin, K. / Arseniev, A. / Goncharuk, S. / Mineev, K.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structural Basis of p75 Transmembrane Domain Dimerization.
Authors: Nadezhdin, K.D. / Garcia-Carpio, I. / Goncharuk, S.A. / Mineev, K.S. / Arseniev, A.S. / Vilar, M.
History
DepositionJan 15, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 16
B: Tumor necrosis factor receptor superfamily member 16


Theoretical massNumber of molelcules
Total (without water)9,0612
Polymers9,0612
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)10 / 10target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Tumor necrosis factor receptor superfamily member 16 / Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor ...Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor / NGF receptor / p75 ICD


Mass: 4530.276 Da / Num. of mol.: 2 / Fragment: UNP residues 245-284 / Mutation: C14A, C36S chain A, C114A, C136S chain B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ngfr, Tnfrsf16 / Plasmid: pGEMEX-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07174

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1712D 1H-13C HSQC aromatic
1813D HN(CO)CA

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Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] p75-TM-C257A, 30 mM [U-98% 2H] DPC, 20 mM sodium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMp75-TM-C257A-1[U-100% 13C; U-100% 15N]1
30 mMDPC-2[U-98% 2H]1
20 mMsodium phosphate-31
Sample conditionspH: 5.9 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOS-NYang Shen, and Ad Baxangles constrains prediction
CARAKeller, Rchemical shift assignment
CARAKeller, Rdata analysis
CARAKeller, Rpeak picking
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
qMDDMayzel M, Orekhov V.processing
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10 / Conformers submitted total number: 10

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