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Yorodumi- PDB-1m7e: Crystal structure of the phosphotyrosine binding domain(PTB) of m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7e | ||||||
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Title | Crystal structure of the phosphotyrosine binding domain(PTB) of mouse Disabled 2(Dab2):implications for Reeling signaling | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PTB / Protein-peptide complex | ||||||
Function / homology | Function and homology information Formyl peptide receptors bind formyl peptides and many other ligands / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / TRAF6 mediated NF-kB activation / ECM proteoglycans / Advanced glycosylation endproduct receptor signaling / amyloid-beta complex / TAK1-dependent IKK and NF-kappa-B activation / growth cone lamellipodium / Post-translational protein phosphorylation ...Formyl peptide receptors bind formyl peptides and many other ligands / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / TRAF6 mediated NF-kB activation / ECM proteoglycans / Advanced glycosylation endproduct receptor signaling / amyloid-beta complex / TAK1-dependent IKK and NF-kappa-B activation / growth cone lamellipodium / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to norepinephrine stimulus / Platelet degranulation / Formation of annular gap junctions / growth cone filopodium / endosome to plasma membrane transport vesicle / Gap junction degradation / positive regulation of clathrin-dependent endocytosis / positive regulation of endothelin production / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / renal protein absorption / positive regulation of integrin-mediated signaling pathway / clathrin coat of coated pit / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / clathrin-coated vesicle membrane / clathrin coat assembly / lipoprotein particle / peptidase activator activity / growth factor receptor binding / Cargo recognition for clathrin-mediated endocytosis / regulation of amyloid-beta clearance / clathrin adaptor activity / Clathrin-mediated endocytosis / astrocyte projection / myeloid cell differentiation / ion binding / regulation of epidermal growth factor-activated receptor activity / frizzled binding / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / axo-dendritic transport / synaptic assembly at neuromuscular junction / G alpha (q) signalling events / smooth endoplasmic reticulum calcium ion homeostasis / heparan sulfate proteoglycan binding / G alpha (i) signalling events / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / negative regulation of protein localization to plasma membrane / mating behavior / cargo receptor activity / response to steroid hormone / ciliary rootlet / hematopoietic stem cell proliferation / main axon / PTB domain binding / Golgi-associated vesicle / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / neuron remodeling / clathrin binding / positive regulation of receptor recycling / : / nuclear envelope lumen / suckling behavior / presynaptic active zone / dendrite development / COPII-coated ER to Golgi transport vesicle / neuronal dense core vesicle / positive regulation of endocytosis / modulation of excitatory postsynaptic potential / apolipoprotein binding / positive regulation of receptor internalization / neuromuscular process controlling balance / regulation of presynapse assembly / transition metal ion binding / positive regulation of cell adhesion / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / cellular response to manganese ion / positive regulation of calcium-mediated signaling / positive regulation of epithelial to mesenchymal transition / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway / cellular response to cAMP / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / forebrain development / Notch signaling pathway Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SIR / Resolution: 2.45 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 | 1m7e.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7e.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7e ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7e | HTTPS FTP |
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-Related structure data
Related structure data | 1oqnC 1p3rC 1m7f 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: 18042.629 Da / Num. of mol.: 3 Fragment: Phosphotyrosine binding domain (PTB), Residues 33-191 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: P98078 #2: Protein/peptide | Mass: 1086.132 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P08592*PLUS #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: 3.66 Å3/Da / Density % sol: 66.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: sodium formate, pH 8.5, 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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Sep 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. all: 31089 / Num. obs: 31089 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 22.9 % / Rsym value: 0.1 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.45→2.5 Å / % possible all: 88.2 |
Reflection | *PLUS Num. measured all: 712193 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 88.2 % |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.272 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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