+Open data
-Basic information
Entry | Database: PDB / ID: 8oyd | ||||||
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Title | TrkB transmembrane domain NMR structure in DMPC/DHPC bicelles | ||||||
Components | BDNF/NT-3 growth factors receptor | ||||||
Keywords | TRANSFERASE / PROTEIN / RECEPTOR / NEUROTROPHIN / BDNF / NT-4 / TMD / DIMER | ||||||
Function / homology | Function and homology information brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / brain-derived neurotrophic factor binding ...brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / brain-derived neurotrophic factor binding / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / NGF-independant TRKA activation / myelination in peripheral nervous system / Activated NTRK2 signals through PI3K / glutamate secretion / feeding behavior / neuronal action potential propagation / positive regulation of synapse assembly / positive regulation of axonogenesis / regulation of GTPase activity / central nervous system neuron development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / oligodendrocyte differentiation / negative regulation of amyloid-beta formation / negative regulation of anoikis / Activated NTRK2 signals through RAS / vasculogenesis / Activated NTRK2 signals through FRS2 and FRS3 / axon terminus / cellular response to brain-derived neurotrophic factor stimulus / learning / long-term synaptic potentiation / cellular response to amino acid stimulus / neuron migration / neuron differentiation / terminal bouton / receptor protein-tyrosine kinase / cerebral cortex development / positive regulation of neuron projection development / circadian rhythm / positive regulation of peptidyl-serine phosphorylation / early endosome membrane / protease binding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / dendritic spine / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / positive regulation of protein phosphorylation / axon / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kot, E.F. / Mineev, K.S. / Goncharuk, S.A. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Structural Basis for the transmembrane signaling and antidepressant-induced activation of the receptor tyrosine kinase TrkB Authors: Kot, E.F. / Mineev, K.S. / Goncharuk, S.A. / Vilar, M. / Franco, M.L. / Benito-Martinez, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oyd.cif.gz | 288.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oyd.ent.gz | 241.8 KB | Display | PDB format |
PDBx/mmJSON format | 8oyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/8oyd ftp://data.pdbj.org/pub/pdb/validation_reports/oy/8oyd | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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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/peptide | Mass: 4975.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: In the constraint files, the local numeration starts from M1 for chain A and from M101 for chain B. Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK2, TRKB / Variant: TK+ / Plasmid: pGEMEX-1 Cell (production host): Cell-free expression system, lysate-based Production host: Escherichia coli (E. coli) References: UniProt: Q16620, receptor protein-tyrosine kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: bicelle Contents: 5 % v/v [U-2H] D2O, 1.1 mM [U-100% 13C; U-100% 15N] High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), 9.6 mM [U-2H] DMPC, 42.7 mM [U-2H] DHPC, 1.0 mM n. ...Contents: 5 % v/v [U-2H] D2O, 1.1 mM [U-100% 13C; U-100% 15N] High affinity receptor of neurotrophin-4 and brain-derived neurotrophic factor (TrkB), 9.6 mM [U-2H] DMPC, 42.7 mM [U-2H] DHPC, 1.0 mM n.a. TCEP, 0.01 % w/v n.a. sodium azide, 20.0 mM n.a. sodium phosphate buffer, 0.5 mM d4 TSP, 95% H2O/5% D2O Label: 13C-15N-labeled TrkBtm / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 20 mM / Ionic strength err: 0.1 / Label: bicelles / pH: 6.0 / PH err: 0.1 / Pressure: AMBIENT Pa / Temperature: 313 K / Temperature err: 0.1 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 |