+
Open data
-
Basic information
Entry | Database: PDB / ID: 7u01 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of CD148 fibronectin type III domain 2 | |||||||||
![]() | Receptor-type tyrosine-protein phosphatase eta | |||||||||
![]() | SIGNALING PROTEIN / receptor type protein tyrosine phosphatase | |||||||||
Function / homology | ![]() positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway ...positive regulation of Fc receptor mediated stimulatory signaling pathway / contact inhibition / gamma-catenin binding / delta-catenin binding / platelet-derived growth factor receptor binding / positive regulation of platelet activation / negative regulation of vascular permeability / negative regulation of platelet-derived growth factor receptor signaling pathway / mitogen-activated protein kinase binding / negative regulation of T cell receptor signaling pathway / positive regulation of macrophage chemotaxis / positive chemotaxis / negative regulation of epidermal growth factor receptor signaling pathway / Phosphorylation of CD3 and TCR zeta chains / oligodendrocyte differentiation / phosphatase activity / positive regulation of focal adhesion assembly / platelet-derived growth factor receptor signaling pathway / : / immunological synapse / positive regulation of cell adhesion / peptidyl-tyrosine dephosphorylation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of cell adhesion / specific granule membrane / positive regulation of phagocytosis / Negative regulation of FLT3 / negative regulation of insulin receptor signaling pathway / negative regulation of cell migration / protein-tyrosine-phosphatase / B cell differentiation / negative regulation of MAP kinase activity / protein tyrosine phosphatase activity / Negative regulation of MET activity / negative regulation of cell growth / beta-catenin binding / cytokine-mediated signaling pathway / ruffle membrane / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / blood coagulation / glucose homeostasis / heart development / T cell receptor signaling pathway / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cadherin binding / negative regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhou, D. / Zhu, J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure of CD148 fibronectin type III domain 1 and 2 Authors: Zhou, D. / Zhu, J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 207.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.7 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u08C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
4 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 16958.318 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.29 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M sodium acetate pH4.5, 3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979276 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→50 Å / Num. obs: 26929 / % possible obs: 100 % / Redundancy: 26.6 % / Biso Wilson estimate: 54.4779195349 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.2971→2.3545 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 1712 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.786072096 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29707910798→45.7113330479 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 116.185225815 Å / Origin y: 76.2849144805 Å / Origin z: 19.365837285 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |