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Yorodumi- PDB-1ow8: Paxillin LD2 motif bound to the Focal Adhesion Targeting (FAT) do... -
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-Basic information
Entry | Database: PDB / ID: 1ow8 | ||||||
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Title | Paxillin LD2 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase | ||||||
Components |
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Keywords | TRANSFERASE / 4 helical bundle / amphiphatic helix | ||||||
Function / homology | Function and homology information netrin-activated signaling pathway / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / vinculin binding / detection of muscle stretch / neuropilin binding / positive regulation of ubiquitin-dependent protein catabolic process ...netrin-activated signaling pathway / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / vinculin binding / detection of muscle stretch / neuropilin binding / 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 / microtubule associated complex / 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 / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / Smooth Muscle Contraction / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / GAB1 signalosome / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of cell adhesion / heart morphogenesis / stress fiber / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / Integrin signaling / substrate adhesion-dependent cell spreading / 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 / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell-cell junction / cell migration / integrin binding / lamellipodium / 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 / cell adhesion / 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 / signal transduction / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Hoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Werner, J.M. / Arold, S.T. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Molecular Recognition of Paxillin LD Motifs by the Focal Adhesion Targeting Domain Authors: Hoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Werner, J.M. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ow8.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ow8.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ow8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/1ow8 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/1ow8 | HTTPS FTP |
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-Related structure data
Related structure data | 1ow6C 1ow7C 1k05S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17836.539 Da / Num. of mol.: 3 / Fragment: Focal Adhesion Targeting Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 OR FAK1 OR FAK / Plasmid: pGEX-6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05397, EC: 2.7.1.112 #2: Protein/peptide | Mass: 1542.755 Da / Num. of mol.: 2 / Fragment: Paxillin LD2 motif / Source method: obtained synthetically / Details: Sequence derived from human paxillin / References: UniProt: P49023*PLUS #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: 4.86 Å3/Da / Density % sol: 74.51 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: sodium chloride, glycerol, Hepes, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
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: BM30A / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 30, 2002 Details: two crystals monochromator between two cylindrical parabolic mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→34.5 Å / Num. all: 22456 / Num. obs: 22456 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 82.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.1 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2159 / Rsym value: 0.68 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 82912 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBentry 1K05 Resolution: 2.85→34.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.471 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The second LD2 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other LD2 - ...Details: The second LD2 motif (chain F, bound to molecule C) was fitted into the unbiased 3Fo-2Fc maps (CNS). Its position and orientation were inferred from homology with the well-defined other LD2 - FAT interaction (chains A and C), and are supported by NMR data (see publication).
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.913 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→34.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20 /
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Refinement | *PLUS % reflection Rfree: 7 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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