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Yorodumi- PDB-3gm3: Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gm3 | ||||||
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Title | Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 | ||||||
Components | Protein tyrosine kinase 2 beta | ||||||
Keywords | TRANSFERASE / four-helix bundle | ||||||
Function / homology | Function and homology information regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / apical dendrite / oocyte maturation / positive regulation of ubiquitin-dependent protein catabolic process / activation of Janus kinase activity / regulation of release of sequestered calcium ion into cytosol / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / sprouting angiogenesis / Interleukin-2 signaling / long-term synaptic depression / regulation of NMDA receptor activity / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / postsynaptic density, intracellular component / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / positive regulation of protein kinase activity / glial cell proliferation / cellular defense response / response to glucose / vascular endothelial growth factor receptor signaling pathway / response to mechanical stimulus / regulation of cell adhesion / peptidyl-tyrosine autophosphorylation / cellular response to retinoic acid / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / response to hormone / positive regulation of synaptic transmission, glutamatergic / positive regulation of endothelial cell migration / positive regulation of translation / response to cocaine / long-term synaptic potentiation / response to ischemia / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / regulation of synaptic plasticity / non-membrane spanning protein tyrosine kinase activity / response to hydrogen peroxide / Schaffer collateral - CA1 synapse / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / VEGFA-VEGFR2 Pathway / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / neuron projection development / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / presynapse / lamellipodium / cell body / cell cortex / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / growth cone / positive regulation of cell growth / protein tyrosine kinase activity / protein-containing complex assembly / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / protein autophosphorylation / postsynaptic density / adaptive immune response / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cytoskeleton Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lulo, J.E. / Yuzawa, S. / Schlessinger, J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Crystal structures of free and ligand-bound focal adhesion targeting domain of Pyk2 Authors: Lulo, J. / Yuzawa, S. / Schlessinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gm3.cif.gz | 36.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gm3.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gm3 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gm3 | HTTPS FTP |
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-Related structure data
Related structure data | 3gm1C 3gm2SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16692.205 Da / Num. of mol.: 1 Fragment: Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009 Mutation: C899A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q14289, non-specific protein-tyrosine kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2006 |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 5467 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GM2 Resolution: 2.6→32.38 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.447 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.704 / ESU R Free: 0.345 / 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: 38.947 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.599→2.666 Å / Total num. of bins used: 20
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