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Yorodumi- PDB-3gm1: Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of... -
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-Basic information
Entry | Database: PDB / ID: 3gm1 | ||||||
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Title | Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides | ||||||
Components |
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Keywords | TRANSFERASE / four-helix bundle / LD4 motif | ||||||
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 / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / negative regulation of bone mineralization / negative regulation of muscle cell apoptotic process / vinculin binding / cortical cytoskeleton organization / neuropilin binding / 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 / microtubule associated complex / positive regulation of cell-matrix adhesion / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / 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 / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / negative regulation of potassium ion transport / RHOU GTPase cycle / response to immobilization stress / endothelial cell migration / Smooth Muscle Contraction / positive regulation of protein kinase activity / glial cell proliferation / GAB1 signalosome / cellular defense response / response to glucose / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / response to mechanical stimulus / regulation of cell adhesion / stress fiber / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / positive regulation of stress fiber assembly / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / response to hormone / positive regulation of synaptic transmission, glutamatergic / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of translation / response to cocaine / long-term synaptic potentiation / integrin-mediated signaling pathway / response to ischemia / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / regulation of synaptic plasticity / non-specific protein-tyrosine kinase / Schaffer collateral - CA1 synapse / non-membrane spanning protein tyrosine kinase activity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / response to calcium ion / peptidyl-tyrosine phosphorylation / neuron projection development / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / cell migration / presynapse / lamellipodium Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 3gm1.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gm1.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gm1 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gm1 | HTTPS FTP |
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-Related structure data
Related structure data | 3gm2SC 3gm3C 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16692.205 Da / Num. of mol.: 2 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 #2: Protein/peptide | Mass: 1436.609 Da / Num. of mol.: 4 / Fragment: Paxillin LD4 Motif, UNP residues 262-274 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: P49023 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 4.1 M NaCl, 100 mM HEPES, 5% glycerol, pH 6.3, 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: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2005 |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 9532 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.95→3.06 Å / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GM2 Resolution: 2.95→42.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.693 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / 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: 56.162 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→42.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.027 Å / Total num. of bins used: 20
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