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Yorodumi- PDB-3zdt: Crystal structure of basic patch mutant FAK FERM domain FAK31- 40... -
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-Basic information
Entry | Database: PDB / ID: 3zdt | ||||||
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Title | Crystal structure of basic patch mutant FAK FERM domain FAK31- 405 K216A, K218A, R221A, K222A | ||||||
Components | FOCAL ADHESION KINASE 1 | ||||||
Keywords | TRANSFERASE / CELL ADHESION | ||||||
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 / DCC mediated attractive signaling / 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 / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / regulation of cell adhesion / response to muscle stretch / ciliary basal body / molecular function activator activity / actin filament organization / epidermal growth factor receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / sarcolemma / integrin binding / positive regulation of protein binding / cell cortex / protein tyrosine kinase activity / protease binding / protein autophosphorylation / dendritic spine / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Goni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Martin, M.T. / Eck, M.J. / Kremer, L. / Graeter, F. / Gervasio, F.L. ...Goni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Martin, M.T. / Eck, M.J. / Kremer, L. / Graeter, F. / Gervasio, F.L. / Perez-Moreno, M. / Lietha, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Phosphatidylinositol 4,5-Bisphosphate Triggers Activation of Focal Adhesion Kinase by Inducing Clustering and Conformational Changes. Authors: Goni, G.M. / Epifano, C. / Boskovic, J. / Camacho-Artacho, M. / Zhou, J. / Bronowska, A. / Martin, M.T. / Eck, M.J. / Kremer, L. / Grater, F. / Gervasio, F.L. / Perez-Moreno, M. / Lietha, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zdt.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zdt.ent.gz | 225.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zdt_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 3zdt_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 3zdt_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 3zdt_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdt ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdt | HTTPS FTP |
-Related structure data
Related structure data | 4cyeC 2al6S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42898.531 Da / Num. of mol.: 2 / Fragment: FERM DOMAIN, RESIDUES 31-405 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q00944, non-specific protein-tyrosine kinase #2: Water | ChemComp-HOH / | Sequence details | K216A, K218A, R221A, K222A | |
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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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 14% PEG4K, 200 MM MGCL2, 100 MM TRIS PH 8.5, 10 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07214 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07214 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 14023 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.15→3.34 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AL6 Resolution: 3.15→43.88 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.881 / SU B: 62.884 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.543 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.6 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→43.88 Å
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