+Open data
-Basic information
Entry | Database: PDB / ID: 2mic | ||||||
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Title | NMR structure of p75 transmembrane domain in DPC micelles | ||||||
Components | Tumor necrosis factor receptor superfamily member 16 | ||||||
Keywords | MEMBRANE PROTEIN / dimer / transmembrane / p75 | ||||||
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 | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Nadezhdin, K. / Arseniev, A. / Goncharuk, S. / Mineev, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mic.cif.gz | 257.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mic.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/2mic ftp://data.pdbj.org/pub/pdb/validation_reports/mi/2mic | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4562.341 Da / Num. of mol.: 2 / Fragment: UNP residues 245-284 / Mutation: C36S (chain A), 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.9 mM [U-100% 13C; U-100% 15N] p75-TM-wt, 95 mM [U-98% 2H] DPC, 20 mM sodium phosphate, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | pH: 5.9 / Pressure: ambient / Temperature: 318 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | Protein chi angle constraints total count: 10 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 42 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10 |