+Open data
-Basic information
Entry | Database: PDB / ID: 1qvx | |||||||||
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Title | SOLUTION STRUCTURE OF THE FAT DOMAIN OF FOCAL ADHESION KINASE | |||||||||
Components | Focal adhesion kinase 1PTK2 | |||||||||
Keywords | TRANSFERASE / FOCAL ADHESION KINASE / FAK / FOCAL ADHENSION TARGETING DOMAIN / FAT / HELIX BUNDLE | |||||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / actin filament organization / molecular function activator activity / sarcolemma / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / integrin binding / cell cortex / positive regulation of protein binding / angiogenesis / protein tyrosine kinase activity / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / nucleus / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | SOLUTION NMR / The program CNS version 1.1 with ARIA version 1.2 module was used to calculate the structures of the avian FAT domain. | |||||||||
Authors | Gao, G. / Prutzman, K.C. / King, M.L. / DeRose, E.F. / London, R.E. / Schaller, M.D. / Campbell, S.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: NMR Solution Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase in Complex with a Paxillin LD Peptide: EVIDENCE FOR A TWO-SITE BINDING MODEL. Authors: Gao, G. / Prutzman, K.C. / King, M.L. / Scheswohl, D.M. / DeRose, E.F. / London, R.E. / Schaller, M.D. / Campbell, S.L. | |||||||||
History |
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Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qvx.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1qvx.ent.gz | 872.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qvx ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qvx | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15000.480 Da / Num. of mol.: 1 / Fragment: FAT DOMAIN (RESIDUES 920-1053) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: FAK / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q00944, EC: 2.7.1.112 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Aromatic sidechain assignments were obtained from 2D (HB)CB(CGCDCE)HE and 2D (HB)CB(CGCD)HD experiments. 1H-15N residual dipolar coupling values were measured using 7.5 mg/ml Pf1 phage as aligning medium |
-Sample preparation
Details | Contents: 0.6mM 13C,15N labeled FAT with 4.8mM LD2 peptide, 25mM TRIS-MALEATE, 0.1% NAN3, 1.0uM PPACK, 0.5mg/mL PEFABLOC, 90% H2O, 10% D2O Solvent system: 20mM deuterated Tris-maleate, 50mM NaCl, 0.1mM EDTA, 0.1% NaN3, and 10% D2O, pH 6.0 |
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Sample conditions | Ionic strength: 50 mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 310 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: The program CNS version 1.1 with ARIA version 1.2 module was used to calculate the structures of the avian FAT domain. Software ordinal: 1 Details: The structural restraints included NOE, hydrogen bond, dihedral angle, and RDC restraints. The NOE distance restraints were derived from a 3D simultaneous 13C/15N edited NOESY peak lists ...Details: The structural restraints included NOE, hydrogen bond, dihedral angle, and RDC restraints. The NOE distance restraints were derived from a 3D simultaneous 13C/15N edited NOESY peak lists with 75 ms mixing time. The peak lists were generated automatically by NMRView and edited manually to remove any obvious water and apodization artifacts. The peak lists were unassigned and uncalibrated with respect to distance. To calibrate the NOE distances, the rotational correlation time of the complex was set to 10 ns and was based on values obtained on proteins of this size at similar temperature. The default parameters for ARIA produced structures with poor convergence. Several parameters were optimized, including the ambiguous cutoff (rho), the violation tolerance (vtol), and maximum number of ambiguities per peak (maxn), to provide better noise discrimination. The following scheme led to the best convergence over 9 iterations: rho = (0.95, 0.95, 0.95, 0.94, 0.93, 0.92, 0.91, 0.90, 0 80), vtol = (5.0, 2.0, 1.0, 0.5, 0.25, 1.0, 0.1, 0.1, 0.1), maxn = 5 for all iterations. An ensemble of 25 calculated NMR structures of the avian FAT domain was selected for further analysis. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 25 |