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Yorodumi- PDB-1p3r: Crystal structure of the phosphotyrosin binding domain(PTB) of mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p3r | ||||||
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Title | Crystal structure of the phosphotyrosin binding domain(PTB) of mouse Disabled 1(Dab1) | ||||||
Components | Disabled homolog 2 | ||||||
Keywords | SIGNALING PROTEIN / PTB | ||||||
Function / homology | Function and homology information positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / Formation of annular gap junctions / Gap junction degradation / positive regulation of clathrin-dependent endocytosis / renal protein absorption / AP-2 adaptor complex binding / positive regulation of integrin-mediated signaling pathway / clathrin coat of coated pit / clathrin coat assembly ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / Formation of annular gap junctions / Gap junction degradation / positive regulation of clathrin-dependent endocytosis / renal protein absorption / AP-2 adaptor complex binding / positive regulation of integrin-mediated signaling pathway / clathrin coat of coated pit / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated vesicle membrane / clathrin adaptor activity / Clathrin-mediated endocytosis / myeloid cell differentiation / negative regulation of protein localization to plasma membrane / response to steroid hormone / cargo receptor activity / hematopoietic stem cell proliferation / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of receptor recycling / positive regulation of endocytosis / positive regulation of receptor internalization / positive regulation of cell adhesion / positive regulation of epithelial to mesenchymal transition / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway / clathrin-coated pit / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / receptor-mediated endocytosis / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of transcription elongation by RNA polymerase II / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / negative regulation of cell growth / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / negative regulation of epithelial cell proliferation / integrin binding / protein transport / negative regulation of neuron projection development / in utero embryonic development / positive regulation of cell migration / apical plasma membrane / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1p3r.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p3r.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/1p3r ftp://data.pdbj.org/pub/pdb/validation_reports/p3/1p3r | HTTPS FTP |
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-Related structure data
Related structure data | 1m7eSC 1oqnC 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: 18042.629 Da / Num. of mol.: 3 / Fragment: PTB domain of mouse Disabled 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: DAB2 OR DOC2 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98078 #2: 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: 3.97 Å3/Da / Density % sol: 69.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium formate, 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: 1.02466 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 8, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02466 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 49672 / % possible obs: 97.1 % / Observed criterion σ(I): -1 / Redundancy: 13.5 % / Rsym value: 0.084 / Net I/σ(I): 54.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 54.7 % / Num. measured all: 2717217 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M7E Resolution: 2.1→30 Å / σ(F): 1.5 /
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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