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Yorodumi- PDB-3u3f: Structural basis for the interaction of Pyk2 PAT domain with paxi... -
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-Basic information
Entry | Database: PDB / ID: 3u3f | ||||||
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Title | Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs | ||||||
Components |
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Keywords | TRANSFERASE/signaling protein / 4-helix bundle / focal adhesion / tyrosine kinase / paxillin / TRANSFERASE-signaling protein complex | ||||||
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 / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation ...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 / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / 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 / vinculin binding / cortical cytoskeleton organization / neuropilin binding / apical dendrite / positive regulation of ubiquitin-dependent protein catabolic process / regulation of release of sequestered calcium ion into cytosol / activation of Janus kinase activity / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / oocyte maturation / long-term synaptic depression / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / microtubule associated complex / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / 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 / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / endothelial cell migration / Smooth Muscle Contraction / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / GAB1 signalosome / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / response to mechanical stimulus / 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 / positive regulation of endothelial cell migration / positive regulation of synaptic transmission, glutamatergic / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / response to cocaine / response to hormone / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / 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 / cell-cell junction / cell migration / presynapse / lamellipodium Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å | ||||||
Authors | Vanarotti, M. / Miller, D.J. / Guibao, C.C. / Zheng, J.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structural and Mechanistic Insights into the Interaction between Pyk2 and Paxillin LD Motifs. Authors: Vanarotti, M.S. / Miller, D.J. / Guibao, C.D. / Nourse, A. / Zheng, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u3f.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u3f.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 3u3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u3f ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u3f | HTTPS FTP |
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-Related structure data
Related structure data | 2lk4C 4r32C 3gm1S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15260.584 Da / Num. of mol.: 4 / Fragment: unp residues 871-1005 / Mutation: C899S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q14289, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1915.128 Da / Num. of mol.: 6 / Fragment: unp residues 261-277 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / 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: 4.12 Å3/Da / Density % sol: 70.11 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING ...Details: The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2011 / Details: mirrors |
Radiation | Monochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. all: 22414 / Num. obs: 21900 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 106.2 Å2 / Rsym value: 0.06 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 2076 / Rsym value: 0.647 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3GM1 Resolution: 3.101→29.848 Å / SU ML: 0.3 / σ(F): 0.08 / Phase error: 29.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.391 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.101→29.848 Å
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Refine LS restraints |
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LS refinement shell |
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