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- PDB-1m7e: Crystal structure of the phosphotyrosine binding domain(PTB) of m... -
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Open data
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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 | ||||||
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![]() | SIGNALING PROTEIN / PTB / Protein-peptide complex | ||||||
Function / homology | ![]() Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / ECM proteoglycans / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / growth cone lamellipodium / Post-translational protein phosphorylation ...Formyl peptide receptors bind formyl peptides and many other ligands / amyloid-beta complex / positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / ECM proteoglycans / 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 / Formation of annular gap junctions / growth cone filopodium / Gap junction degradation / positive regulation of clathrin-dependent endocytosis / positive regulation of endothelin production / Lysosome Vesicle Biogenesis / renal protein absorption / AP-2 adaptor complex binding / positive regulation of integrin-mediated signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / clathrin coat of coated pit / lipoprotein particle / regulation of amyloid-beta clearance / peptidase activator activity / growth factor receptor binding / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / clathrin-coated vesicle membrane / clathrin adaptor activity / Clathrin-mediated endocytosis / astrocyte projection / myeloid cell differentiation / ion binding / regulation of epidermal growth factor-activated receptor activity / frizzled binding / 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 / signaling receptor activator activity / heparan sulfate proteoglycan binding / smooth endoplasmic reticulum calcium ion homeostasis / G alpha (q) signalling events / axon midline choice point recognition / astrocyte activation involved in immune response / G alpha (i) signalling events / negative regulation of protein localization to plasma membrane / regulation of spontaneous synaptic transmission / mating behavior / response to steroid hormone / cargo receptor activity / ciliary rootlet / PTB domain binding / hematopoietic stem cell proliferation / Golgi-associated vesicle / main axon / positive regulation of amyloid fibril formation / neuron remodeling / low-density lipoprotein particle receptor binding / clathrin binding / : / positive regulation of receptor recycling / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / neuronal dense core vesicle / modulation of excitatory postsynaptic potential / positive regulation of endocytosis / apolipoprotein binding / positive regulation of receptor internalization / neuromuscular process controlling balance / regulation of presynapse assembly / transition metal ion binding / positive regulation of cell adhesion / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / cellular response to manganese ion / positive regulation of epithelial to mesenchymal transition / positive regulation of calcium-mediated signaling / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / clathrin-coated pit / positive regulation of substrate adhesion-dependent cell spreading / regulation of peptidyl-tyrosine phosphorylation / cellular response to cAMP / forebrain development Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yun, M. / Keshvara, L. / Park, C.-G. / Zhang, Y.-M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.-W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.4 KB | Display | ![]() |
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PDB format | ![]() | 84.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.7 KB | Display | ![]() |
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Full document | ![]() | 408.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oqnC ![]() 1p3rC ![]() 1m7f C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() |
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 % |
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Processing
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Refinement | Method to determine structure: ![]()
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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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