+Open data
-Basic information
Entry | Database: PDB / ID: 8z10 | ||||||
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Title | Human beta-catenin crystal structure | ||||||
Components | Catenin beta-1 | ||||||
Keywords | STRUCTURAL PROTEIN / Beta-catenin / BCL9 | ||||||
Function / homology | Function and homology information CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 / neural plate development / glial cell fate determination / 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 / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / embryonic axis specification / endodermal cell fate commitment / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / 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 / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / 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 / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / negative regulation of protein sumoylation / adherens junction assembly / embryonic heart tube development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Adherens junctions interactions / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Tim, F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Beta-catenin Authors: Tim, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8z10.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8z10.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 8z10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/8z10 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/8z10 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60187.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / References: UniProt: P35222 | ||
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#2: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Apo crystals of beta-Catenin were grown from 14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline. Crystal was transferred into a soaking solution and incubated at RT for 4 days. Crystals were ...Details: Apo crystals of beta-Catenin were grown from 14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline. Crystal was transferred into a soaking solution and incubated at RT for 4 days. Crystals were transferred into cryoprotectant (14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol), and then flash frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 26005 / % possible obs: 99.28 % / Redundancy: 2.6 % / CC1/2: 0.997 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.35→2.39 Å / Num. unique obs: 2467 / Rpim(I) all: 0.06 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→6.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.277 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.37 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→6.37 Å
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