+Open data
-Basic information
Entry | Database: PDB / ID: 4ev8 | ||||||
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Title | Crystal structure of mouse catenin beta-59 in 2.4M urea. | ||||||
Components | Catenin beta-1 | ||||||
Keywords | CELL ADHESION / mouse catenin | ||||||
Function / homology | Function and homology information lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / : / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / : / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / hair cycle process / positive regulation of epithelial cell differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / TCF dependent signaling in response to WNT / mesenchyme development / Formation of the beta-catenin:TCF transactivating complex / trachea morphogenesis / endoderm formation / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / VEGFR2 mediated vascular permeability / neural plate development / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / animal organ development / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / central nervous system vasculogenesis / Ca2+ pathway / regulation of epithelial cell differentiation / Schwann cell proliferation / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / RHO GTPases activate IQGAPs / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / Scrib-APC-beta-catenin complex / morphogenesis of embryonic epithelium / positive regulation of fibroblast growth factor receptor signaling pathway / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / sympathetic ganglion development / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / delta-catenin binding / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / mesenchymal cell proliferation involved in lung development / smooth muscle cell differentiation / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / presynaptic active zone cytoplasmic component / cell projection membrane / mesenchymal cell proliferation / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / establishment of blood-brain barrier / tissue homeostasis Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, C. / Zhang, G.Y. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of mouse catenin beta-59 in 2.4M urea. Authors: Wang, C. / Zhang, G.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ev8.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ev8.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ev8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/4ev8 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4ev8 | HTTPS FTP |
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-Related structure data
Related structure data | 3bctS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58844.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q02248 | ||
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#2: Chemical | ChemComp-URE / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010 |
Radiation | Monochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.5 Å / Num. obs: 48834 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.072 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BCT Resolution: 1.9→35.47 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.82 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→35.47 Å
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Refine LS restraints |
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LS refinement shell |
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