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Yorodumi- PDB-1y19: Structural basis for phosphatidylinositol phosphate kinase type I... -
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-Basic information
Entry | Database: PDB / ID: 1y19 | ||||||
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Title | Structural basis for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / SIGNALING PROTEIN / FOCAL ADHESION / FERM DOMAIN / CYTOSKELETON / NPXY MOTIF / PTB DOMAIN | ||||||
Function / homology | Function and homology information 1-phosphatidylinositol-4-phosphate 5-kinase / presynaptic endocytic zone membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Synthesis of PIPs at the plasma membrane ...1-phosphatidylinositol-4-phosphate 5-kinase / presynaptic endocytic zone membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Synthesis of PIPs at the plasma membrane / uropod / Platelet degranulation / LIM domain binding / phosphatidylinositol metabolic process / vinculin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Clathrin-mediated endocytosis / integrin activation / phosphatidylinositol biosynthetic process / cell-substrate junction assembly / regulation of postsynaptic neurotransmitter receptor internalization / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / phagocytic cup / phosphatidylserine binding / exocytosis / phosphatidylinositol phosphate biosynthetic process / phagocytosis / ruffle / phosphatidylinositol binding / axonogenesis / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / cell-cell adhesion / platelet aggregation / ruffle membrane / chemotaxis / actin filament binding / integrin binding / postsynaptic density / cytoskeleton / endosome membrane / phosphorylation / focal adhesion / glutamatergic synapse / cell surface / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | de Pereda, J.M. / Wegener, K. / Santelli, E. / Bate, N. / Ginsberg, M.H. / Critchley, D.R. / Campbell, I.D. / Liddington, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural bases for phosphatidylinositol phosphate kinase type I-gamma binding to talin at focal adhesions Authors: de Pereda, J.M. / Wegener, K. / Santelli, E. / Bate, N. / Ginsberg, M.H. / Critchley, D.R. / Campbell, I.D. / Liddington, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y19.cif.gz | 253.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y19.ent.gz | 215 KB | Display | PDB format |
PDBx/mmJSON format | 1y19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y19 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y19 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1711.829 Da / Num. of mol.: 6 / Fragment: C-TERMINAL REGION Source method: isolated from a genetically manipulated source Details: chimera of chain A/B, C/D, E/F, G/H, I/J, K/L / Source: (gene. exp.) Mus musculus (house mouse) / Description: FORMS CHIMERA WITH TALIN AT THE N-TERMINUS / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O70161 #2: Protein | Mass: 23281.965 Da / Num. of mol.: 6 / Fragment: F2 AND F3 SUBDOMAINS OF THE FERM DOMAIN Source method: isolated from a genetically manipulated source Details: chimera of chain A/B, C/D, E/F, G/H, I/J, K/L / Source: (gene. exp.) Mus musculus (house mouse) Description: FORMS CHIMERA WITH PHOSPHATIDYL INOSITOL KINASE TYPE 1 GAMMA AT THE C-TERMINUS Gene: Tln1, Tln / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26039 #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: 2.51 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.2 Details: 0.1 M Na/K phosphte buffer, 35% MPD, pH 6.2, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.008 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 43284 / % possible obs: 96.7 % / Observed criterion σ(I): -4 / Redundancy: 2.4 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.4 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å /
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