[English] 日本語
![](img/lk-miru.gif)
- PDB-1ow8: Paxillin LD2 motif bound to the Focal Adhesion Targeting (FAT) do... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ow8 | ||||||
---|---|---|---|---|---|---|---|
Title | Paxillin LD2 motif bound to the Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / 4 helical bundle / amphiphatic helix | ||||||
Function / homology | ![]() netrin-activated signaling pathway / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / vinculin binding / neuropilin binding / positive regulation of ubiquitin-dependent protein catabolic process ...netrin-activated signaling pathway / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / vinculin binding / 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 / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / negative regulation of cell-cell adhesion / regulation of GTPase activity / positive regulation of macrophage chemotaxis / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / regulation of cytoskeleton organization / 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 / Smooth Muscle Contraction / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / positive regulation of protein kinase activity / GAB1 signalosome / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / Integrin signaling / SH2 domain binding / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / molecular function activator activity / integrin-mediated signaling pathway / cell motility / FCGR3A-mediated phagocytosis / axon guidance / non-specific protein-tyrosine kinase / regulation of protein phosphorylation / non-membrane spanning protein tyrosine kinase activity / placenta development / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / beta-catenin binding / VEGFA-VEGFR2 Pathway / cellular response to reactive oxygen species / 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 / protein tyrosine kinase activity / angiogenesis / protein autophosphorylation / dendritic spine / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell adhesion / positive regulation of cell migration / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoellerer, M.K. / Noble, M.E.M. / Labesse, G. / Werner, J.M. / Arold, S.T. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ow6C ![]() 1ow7C ![]() 1k05S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() #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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.86 Å3/Da / Density % sol: 74.51 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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).
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→34.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 7 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|