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- PDB-4xev: Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xev | ||||||
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Title | Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide | ||||||
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![]() | CELL ADHESION / 4-HELIX BUNDLE / FOCAL ADHESION / TYROSINE KINASE / LEUPAXIN | ||||||
Function / homology | ![]() negative regulation of B cell receptor signaling pathway / regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / muscle structure development / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway ...negative regulation of B cell receptor signaling pathway / regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / muscle structure development / 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 / muscle alpha-actinin binding / cortical cytoskeleton organization / apical dendrite / 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 / negative regulation of cell adhesion / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / podosome / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / long-term synaptic depression / oocyte maturation / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / calcium/calmodulin-dependent protein kinase activity / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / filamentous actin / regulation of cell adhesion mediated by integrin / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / endothelial cell migration / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / glutamate receptor binding / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / cellular response to retinoic acid / stress fiber / peptidyl-tyrosine autophosphorylation / bone resorption / 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 hormone / response to cocaine / cell projection / positive regulation of translation / response to ischemia / integrin-mediated signaling pathway / long-term synaptic potentiation / regulation of actin cytoskeleton organization / transcription coregulator activity / adherens junction / 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 / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / Z disc / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / : / positive regulation of reactive oxygen species metabolic process / neuron projection development / MAPK cascade / positive regulation of nitric oxide biosynthetic process / presynapse / lamellipodium / actin binding / heart development / cell cortex / regulation of cell shape Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Interaction between Pyk2-FAT Domain and Leupaxin LD Repeats. Authors: Vanarotti, M.S. / Finkelstein, D.B. / Guibao, C.D. / Nourse, A. / Miller, D.J. / Zheng, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.8 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xefC ![]() 4xekC ![]() 3gm3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 18034.441 Da / Num. of mol.: 2 / Mutation: C899S, C972A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q14289, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 2090.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: The 4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM MES pH 6.5 and 25 % PEG 3000). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 25954 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.039 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.4 / % possible all: 77.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GM3 Resolution: 2.0073→27.263 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.0073→27.263 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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