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Open data
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Basic information
Entry | Database: PDB / ID: 1wwb | ||||||
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Title | LIGAND BINDING DOMAIN OF HUMAN TRKB RECEPTOR | ||||||
![]() | PROTEIN (Brain Derived Neurotrophic Factor Receptor TrkB) | ||||||
![]() | TRANSFERASE / TRK RECEPTOR / RECEPTOR TYROSINE KINASE / 3D-DOMAIN SWAPPING | ||||||
Function / homology | ![]() 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 / oligodendrocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / protein autophosphorylation / dendritic spine / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wiesmann, C. / Ultsch, M.H. / Bass, S.H. / De Vos, A.M. | ||||||
![]() | ![]() Title: Crystal structures of the neurotrophin-binding domain of TrkA, TrkB and TrkC. Authors: Ultsch, M.H. / Wiesmann, C. / Simmons, L.C. / Henrich, J. / Yang, M. / Reilly, D. / Bass, S.H. / de Vos, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.3 KB | Display | ![]() |
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PDB format | ![]() | 23.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.2 KB | Display | ![]() |
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Full document | ![]() | 365 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wwaC ![]() 1wwcSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11802.254 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.34 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Mar 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 115960 / % possible obs: 98.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.019 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WWC Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 Details: THE MOLECULE UNDERGOES 3D-DOMAIN SWAPPING, SUCH THAT STRAND A OF ONE MOLECULE REPLACES THE SAME STRAND A OF A SYMMETRY RELATED MATE
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 0.2 / % reflection Rfree: 9.5 % / Rfactor obs: 0.247 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |