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Yorodumi- PDB-1k04: Crystal Structure of the Focal Adhesion Targeting Domain of Focal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k04 | ||||||
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Title | Crystal Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase | ||||||
Components | FOCAL ADHESION KINASE 1PTK2 | ||||||
Keywords | TRANSFERASE / up-down-up-down four helical bundle forming a helix-exchange dimer | ||||||
Function / homology | Function and homology information netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / negative regulation of cell-cell adhesion / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / Integrin signaling / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / molecular function activator activity / cell motility / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / intracellular membrane-bounded organelle / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Arold, S.T. / Hoellerer, M.K. / Noble, M.E.M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The structural basis of localization and signaling by the focal adhesion targeting domain. Authors: Arold, S.T. / Hoellerer, M.K. / Noble, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k04.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k04.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1k04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k04 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k04 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second protomer of the dimeric assembly is generated by the two fold axis: -X,-Y,1/2+Z |
-Components
#1: Protein | Mass: 17949.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAK / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q05397, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.17 Å3/Da / Density % sol: 42.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES, NaCl, Na/K phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→47.7 Å / Num. obs: 11110 / % possible obs: 94.8 % / Observed criterion σ(F): 0.9 / Observed criterion σ(I): 0.9 / Redundancy: 3.3 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2462 / Rsym value: 0.509 / % possible all: 88.9 |
Reflection | *PLUS Num. measured all: 36960 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.509 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→47.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 7 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.243 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 / Rfactor Rwork: 0.44 |