[English] 日本語
Yorodumi- PDB-4y61: Crystal structure of the complex between Slitrk2 LRR1 and PTP del... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y61 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1 | ||||||
Components |
| ||||||
Keywords | HYDROLASE/SIGNALING PROTEIN / trans-synaptic complex / HYDROLASE-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information : / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / trans-synaptic signaling / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / presynapse assembly / negative regulation of receptor signaling pathway via JAK-STAT ...: / Receptor-type tyrosine-protein phosphatases / Synaptic adhesion-like molecules / trans-synaptic signaling by trans-synaptic complex / trans-synaptic signaling / presynaptic membrane assembly / regulation of postsynaptic density assembly / synaptic membrane adhesion / presynapse assembly / negative regulation of receptor signaling pathway via JAK-STAT / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse organization / regulation of presynapse assembly / GABA-ergic synapse / regulation of immune response / dephosphorylation / hippocampal mossy fiber to CA3 synapse / cell adhesion molecule binding / axonogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / membrane => GO:0016020 / signaling receptor binding / glutamatergic synapse Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.358 Å | ||||||
Authors | Yamgata, A. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Yoshida, T. / Fukai, S. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion. Authors: Yamagata, A. / Sato, Y. / Goto-Ito, S. / Uemura, T. / Maeda, A. / Shiroshima, T. / Yoshida, T. / Fukai, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4y61.cif.gz | 266.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4y61.ent.gz | 214.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y61 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y61 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43772.168 Da / Num. of mol.: 1 / Fragment: UNP residues 21-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprd / Plasmid: pEBMulti-Neo / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q64487, protein-tyrosine-phosphatase |
---|---|
#2: Protein | Mass: 31129.096 Da / Num. of mol.: 1 / Fragment: UNP residues 1-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slitrk2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q810C0 |
#3: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG4000, 0.1 M sodium acetate, 0.1 M MES / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 14509 / % possible obs: 99.2 % / Redundancy: 9.5 % / Rsym value: 0.13 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.35→3.41 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.9 / % possible all: 97.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YD6, 2YD9, 2DJU, and 1OZN Resolution: 3.358→45.654 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 30.07 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.358→45.654 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|