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Yorodumi- PDB-1oqn: Crystal structure of the phosphotyrosine binding domain (PTB) of ... -
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-Basic information
Entry | Database: PDB / ID: 1oqn | ||||||
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Title | Crystal structure of the phosphotyrosine binding domain (PTB) of mouse Disabled 1 (Dab1) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PTB / Inositol / APP | ||||||
Function / homology | Function and homology information cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / lateral motor column neuron migration / ECM proteoglycans / radial glia guided migration of Purkinje cell / Reelin signalling pathway / cerebral cortex radially oriented cell migration / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / lateral motor column neuron migration / ECM proteoglycans / radial glia guided migration of Purkinje cell / Reelin signalling pathway / cerebral cortex radially oriented cell migration / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / growth cone lamellipodium / Post-translational protein phosphorylation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to norepinephrine stimulus / TAK1-dependent IKK and NF-kappa-B activation / Platelet degranulation / growth cone filopodium / cerebellum structural organization / positive regulation of endothelin production / Golgi localization / ventral spinal cord development / radial glia-guided pyramidal neuron migration / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of axonogenesis / motor neuron migration / lipoprotein particle / regulation of amyloid-beta clearance / peptidase activator activity / growth factor receptor binding / negative regulation of receptor signaling pathway via JAK-STAT / regulation of synapse maturation / astrocyte projection / cerebral cortex cell migration / frizzled binding / negative regulation of cell adhesion / regulation of epidermal growth factor-activated receptor activity / astrocyte differentiation / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / heparan sulfate proteoglycan binding / synaptic assembly at neuromuscular junction / signaling receptor activator activity / G alpha (q) signalling events / adult walking behavior / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / G alpha (i) signalling events / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / ciliary rootlet / PTB domain binding / Golgi-associated vesicle / main axon / low-density lipoprotein particle receptor binding / neuron remodeling / positive regulation of amyloid fibril formation / small GTPase-mediated signal transduction / positive regulation of G2/M transition of mitotic cell cycle / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / neuronal dense core vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / regulation of peptidyl-tyrosine phosphorylation / brush border / cell surface receptor signaling pathway via JAK-STAT / apolipoprotein binding / neuromuscular process controlling balance / negative regulation of astrocyte differentiation / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / cellular response to manganese ion / phosphatidylinositol 3-kinase binding / positive regulation of chemokine production / clathrin-coated pit / cellular response to cAMP / forebrain development / Notch signaling pathway / cellular response to copper ion / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / astrocyte activation / positive regulation of neuron differentiation Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yun, M. / Keshvara, L. / Park, C.-G. / Zhang, Y.-M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.-W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structures of the Dab homology domains of mouse disabled 1 and 2 Authors: Yun, M. / Keshvara, L. / Park, C.-G. / Zhang, Y.-M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.-W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oqn.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oqn.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oqn_validation.pdf.gz | 535.7 KB | Display | wwPDB validaton report |
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Full document | 1oqn_full_validation.pdf.gz | 542.8 KB | Display | |
Data in XML | 1oqn_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1oqn_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oqn ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oqn | HTTPS FTP |
-Related structure data
Related structure data | 1m7eSC 1p3rC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 17960.758 Da / Num. of mol.: 2 / Fragment: PTB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97318 #2: Protein/peptide | Mass: 1086.132 Da / Num. of mol.: 2 / Fragment: 9mer peptide / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Rattus norvegicus (rat). References: UniProt: P08592 #3: Chemical | #4: 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: 2.33 Å3/Da / Density % sol: 47.31 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, magnesium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / 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: APS / Beamline: 22-ID / Wavelength: 1.00465 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00465 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 16118 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 24.8 % / Rsym value: 0.077 / Net I/σ(I): 27.3 |
Reflection | *PLUS Num. measured all: 400319 / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M7E Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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