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Yorodumi- PDB-4pbv: Crystal structure of chicken receptor protein tyrosine phosphatas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pbv | ||||||||||||||||||
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Title | Crystal structure of chicken receptor protein tyrosine phosphatase sigma in complex with TrkC | ||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Synapse Cell signalling Cell surface receptor | ||||||||||||||||||
Function / homology | Function and homology information 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 / PIP3 activates AKT signaling ...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 / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / negative regulation of axon extension / heparan sulfate proteoglycan binding / peptidyl-tyrosine dephosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / protein-tyrosine-phosphatase / cellular response to nerve growth factor stimulus / protein tyrosine phosphatase activity / postsynaptic density membrane / receptor protein-tyrosine kinase / positive regulation of neuron projection development / synaptic vesicle membrane / heart development / heparin binding / nervous system development / 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 | Gallus gallus (chicken) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||||||||||||||
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. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Nat Commun / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pbv.cif.gz | 445.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pbv.ent.gz | 364.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pbv_validation.pdf.gz | 506.5 KB | Display | wwPDB validaton report |
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Full document | 4pbv_full_validation.pdf.gz | 510.9 KB | Display | |
Data in XML | 4pbv_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 4pbv_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/4pbv ftp://data.pdbj.org/pub/pdb/validation_reports/pb/4pbv | HTTPS FTP |
-Related structure data
Related structure data | 4pbwC 4pbxC 2yd4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 30399.387 Da / Num. of mol.: 2 / Fragment: Residues 31-302 / Mutation: N163Q, N232Q, N259Q, N267Q and N294Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: NTRK3, TRKC / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) References: UniProt: Q91044, receptor protein-tyrosine kinase #2: Protein | Mass: 32721.014 Da / Num. of mol.: 3 / Fragment: Residues 29-316 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.) Gallus gallus (chicken) / Gene: CRYPalpha1 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q90815, UniProt: F1NWE3*PLUS #3: Sugar | ChemComp-NAG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% PEG 20k, 20% PEG MME 550, 0.1M bicine/Tris pH8.5, 0.03M sodium nitrate, 0.03M disodium hydrogen phosphate, 0.03M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→92.79 Å / Num. obs: 52662 / % possible obs: 99.8 % / Redundancy: 11.6 % / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YD4 Resolution: 2.5→92.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.34 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.405 / ESU R Free: 0.263 / 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: 56.72 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→92.79 Å
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Refine LS restraints |
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