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- PDB-5myb: Homodimerization of Tie2 Fibronectin-like domains 2 and 3 in spac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5myb | |||||||||
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Title | Homodimerization of Tie2 Fibronectin-like domains 2 and 3 in space group P21 | |||||||||
![]() | Angiopoietin-1 receptor | |||||||||
![]() | SIGNALING PROTEIN / receptor / fibronectin-like domains / dimerization / homotypic interactions | |||||||||
Function / homology | ![]() Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation ...Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / regulation of vascular permeability / endochondral ossification / heart trabecula formation / definitive hemopoiesis / sprouting angiogenesis / endothelial cell proliferation / positive regulation of intracellular signal transduction / positive regulation of Rho protein signal transduction / positive regulation of Rac protein signal transduction / growth factor binding / positive regulation of focal adhesion assembly / microvillus / centriolar satellite / negative regulation of endothelial cell apoptotic process / Tie2 Signaling / response to cAMP / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / substrate adhesion-dependent cell spreading / basal plasma membrane / receptor protein-tyrosine kinase / response to peptide hormone / negative regulation of inflammatory response / response to estrogen / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / signaling receptor activity / heart development / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / response to hypoxia / protein kinase activity / phosphorylation / positive regulation of protein phosphorylation / membrane raft / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leppanen, V.-M. / Saharinen, P. / Alitalo, K. | |||||||||
![]() | ![]() Title: Structural basis of Tie2 activation and Tie2/Tie1 heterodimerization. Authors: Leppanen, V.M. / Saharinen, P. / Alitalo, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.2 KB | Display | ![]() |
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PDB format | ![]() | 137.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37583.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn- ...Details: In addition to the Tie2 Fn-like domains, the entity includes mellitin signal peptide, a N-terminal cloning artefact (ADP), C-terminal Factor Xa cleavage site (IEGR) and His-tag. The first Fn-like domain was not in the crystals apparently due to proteolytic removal prior crystallization. Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: Q02763, receptor protein-tyrosine kinase #2: Polysaccharide | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % / Description: rod-like |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris buffer at pH 7.0 - 8.5 and 14-20% PEG 3350 (w/v) Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen cooling system |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014 |
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 104.1 Å2 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.873 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CRYSTAL STRUCTURE OF TIE2 FN-LIKE DOMAINS IN SPACE GROUP C2 Resolution: 2.6→39.8 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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