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- PDB-4pbw: Crystal structure of chicken receptor protein tyrosine phosphatas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pbw | ||||||||||||||||||
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Title | Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC | ||||||||||||||||||
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![]() | SIGNALING PROTEIN / Receptor protein tyrosine phosphatase (RPTP) / Synapse Cell signalling Cell surface receptor | ||||||||||||||||||
Function / homology | ![]() Receptor-type tyrosine-protein phosphatases / NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / negative regulation of collateral sprouting / neurotrophin receptor activity / negative regulation of axon regeneration / negative regulation of dendritic spine development / neurotrophin binding / synaptic membrane adhesion / Activated NTRK3 signals through PI3K ...Receptor-type tyrosine-protein phosphatases / NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / negative regulation of collateral sprouting / neurotrophin receptor activity / negative regulation of axon regeneration / negative regulation of dendritic spine development / neurotrophin binding / synaptic membrane adhesion / Activated NTRK3 signals through PI3K / negative regulation of axon extension / heparan sulfate proteoglycan binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / peptidyl-tyrosine dephosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / phosphorylation / protein-tyrosine-phosphatase / cellular response to nerve growth factor stimulus / protein tyrosine phosphatase activity / postsynaptic density membrane / receptor protein-tyrosine kinase / synaptic vesicle membrane / positive regulation of neuron projection development / nervous system development / heart development / heparin binding / growth cone / perikaryon / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / axon / protein homodimerization activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Coles, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for extracellular cis and trans RPTP sigma signal competition in synaptogenesis. Authors: Coles, C.H. / Mitakidis, N. / Zhang, P. / Elegheert, J. / Lu, W. / Stoker, A.W. / Nakagawa, T. / Craig, A.M. / Jones, E.Y. / Aricescu, A.R. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 555.9 KB | Display | ![]() |
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PDB format | ![]() | 461.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pbvC ![]() 4pbxC ![]() 2yd4S S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 31888.920 Da / Num. of mol.: 3 / Mutation: yes Source method: isolated from a genetically manipulated source Details: Ig3 domain is not visible in electron density, suggesting that this domain had either been proteolytically cleaved during crystallisation or is disordered. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q91044, receptor protein-tyrosine kinase #2: Protein | Mass: 32721.014 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.81 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% w/v PEG MME 5k, 0.1 M HEPES pH 7, 5% w/v Tacsimate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→81.02 Å / Num. obs: 51063 / % possible obs: 96.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3.05→3.13 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.5 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YD4 Resolution: 3.05→94.96 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.915 / SU B: 46.384 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.95 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.246 Å2
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Refinement step | Cycle: 1 / Resolution: 3.05→94.96 Å
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Refine LS restraints |
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