+Open data
-Basic information
Entry | Database: PDB / ID: 4at5 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580 | ||||||
Components | BDNF/NT-3 GROWTH FACTORS RECEPTOR | ||||||
Keywords | TRANSFERASE | ||||||
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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Bertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: The Crystal Structures of Trka and Trkb Suggest Key Regions for Achieving Selective Inhibition. Authors: Bertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4at5.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4at5.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 4at5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4at5_validation.pdf.gz | 661.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4at5_full_validation.pdf.gz | 662.4 KB | Display | |
Data in XML | 4at5_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4at5_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4at5 ftp://data.pdbj.org/pub/pdb/validation_reports/at/4at5 | HTTPS FTP |
-Related structure data
Related structure data | 4aszSC 4at3C 4at4C 4f0iC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34351.695 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 543-838 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q16620, receptor protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-MUJ / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / pH: 8 Details: THE TRKB-GW2580 COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 2.4 M NA-FORMATE, 50 MM HEPES, PH 8.0 AT 4 DEGREES C IN PRESENCE OF 2 MM OF INHIBITOR. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→47.09 Å / Num. obs: 40698 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 16.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.7 / % possible all: 79 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ASZ Resolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.085 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.71 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.154 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→25.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.75 Å / Total num. of bins used: 20
|