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Yorodumi- PDB-1ngr: DEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES ... -
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-Basic information
Entry | Database: PDB / ID: 1ngr | ||||||
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Title | DEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES 334-418, NMR, 20 STRUCTURES | ||||||
Components | P75 LOW AFFINITY NEUROTROPHIN RECEPTOR | ||||||
Keywords | RECEPTOR / P75 / INTRACELLULAR DOMAIN / NEUROTROPHIN RECEPTOR / DEATH DOMAIN | ||||||
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 / negative regulation of dendritic spine development / neurotrophin binding / 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 / nuclear envelope / presynaptic membrane / amyloid-beta binding / cellular response to oxidative stress / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / 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 / VARIABLE TARGET FUNCTION (DIANA) APPROACH | ||||||
Authors | Otting, G. / Liepinsh, E. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: NMR structure of the death domain of the p75 neurotrophin receptor. Authors: Liepinsh, E. / Ilag, L.L. / Otting, G. / Ibanez, C.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ngr.cif.gz | 508.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ngr.ent.gz | 426.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ngr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ngr_validation.pdf.gz | 359.9 KB | Display | wwPDB validaton report |
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Full document | 1ngr_full_validation.pdf.gz | 488.3 KB | Display | |
Data in XML | 1ngr_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 1ngr_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ngr ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ngr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9429.558 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN, RESIDUES 281 - 425 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: NERVE CELLS / Cellular location: CYTOPLASM / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15-(PREP4) / References: UniProt: P07174 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: DISTANCE CONSTRAINTS FROM 3D NOESY-15N-HSQC AND 2D NOESY, COUPLING CONSTANTS FROM 3D HNHA-EXPERIMENT, 2QF-COSY, AND 15N-HSQC. A 15N-LABELED SAMPLE OF P75ICD WAS USED. CONSTRAINTS USED: 914 ...Text: DISTANCE CONSTRAINTS FROM 3D NOESY-15N-HSQC AND 2D NOESY, COUPLING CONSTANTS FROM 3D HNHA-EXPERIMENT, 2QF-COSY, AND 15N-HSQC. A 15N-LABELED SAMPLE OF P75ICD WAS USED. CONSTRAINTS USED: 914 UPPER DISTANCE LIMITS FROM NOE DATA 154 COUPLING CONSTANTS CONSTRAINING DIHEDRAL ANGLES IONIC_STRENGTH: NO SALT ADDED PRESSURE: 1 ATM SOLVENT SYSTEM: 90% H2O/10% D2O |
-Sample preparation
Sample conditions | pH: 7.0 / Temperature: 301 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: VARIABLE TARGET FUNCTION (DIANA) APPROACH / Software ordinal: 1 Details: DIANA MINIMIZATION TO TARGET FUNCTION LESS THAN 1, RESTRAINED ENERGY MINIMIZATION USING OPAL | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST TARGET FUNCTION AFTER DIANA Conformers calculated total number: 50 / Conformers submitted total number: 20 |