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Open data
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Basic information
Entry | Database: PDB / ID: 1i7w | ||||||
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Title | BETA-CATENIN/PHOSPHORYLATED E-CADHERIN COMPLEX | ||||||
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![]() | CELL ADHESION / E-cadherin / beta-catenin / protein-protein complex / extended interface / armadillo repeat / phosphoserine | ||||||
Function / homology | ![]() 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 / uterine epithelium development / 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 / uterine epithelium development / 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 / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / trachea morphogenesis / mesenchyme development / endoderm formation / Formation of the beta-catenin:TCF transactivating complex / VEGFR2 mediated vascular permeability / 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 / Deactivation of the beta-catenin transactivating complex / 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 / regulation of branching involved in salivary gland morphogenesis / Ca2+ pathway / central nervous system vasculogenesis / animal organ development / salivary gland cavitation / regulation of epithelial cell differentiation / Schwann cell proliferation / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / Degradation of beta-catenin by the destruction complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / Degradation of the extracellular matrix / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of cell-cell adhesion / acinar cell differentiation / Integrin cell surface interactions / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / lateral loop / regulation of neuron migration / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / delta-catenin binding / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / negative regulation of axon extension / regulation of osteoclast differentiation / cell-cell adhesion mediated by cadherin / cranial skeletal system development / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, A.H. / Weis, W.I. | ||||||
![]() | ![]() Title: The structure of the beta-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by beta-catenin. Authors: Huber, A.H. / Weis, W.I. #1: ![]() Title: The Cadherin Cytoplasmic Domain is Unstructured in the Absence of Beta-Catenin: A Possible Mechanism for Regulating Cadherin Turnover Authors: Huber, A.H. / Stewart, D.B. / Laurents, D.V. / Nelson, W.J. / Weis, W.I. #2: ![]() Title: Crystal Structure of a Beta-catenin/Tcf Complex Authors: Graham, T.A. / Weaver, C. / Mao, F. / Kimelman, D. / Xu, W. #3: ![]() Title: Three-dimensional Structure of the Armadillo Repeat Region of Beta-catenin Authors: Huber, A.H. / Nelson, W.J. / Weis, W.I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.3 KB | Display | ![]() |
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PDB format | ![]() | 193.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 480.4 KB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 69.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i7xC ![]() 2bctS C: citing same article ( S: Starting model for refinement |
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Similar 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 on special symmetry positions |
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Components
#1: Protein | Mass: 58844.117 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 17243.965 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.45 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: polyethylene glycol monomethylether 5000, Tris-HCl, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2000 Details: 1) Cylindrical 1m long collimating mirror (Rh-coated Si) before monochromator 2) Toroidal focusing mirror 1.2m long (Rh-coated zerodur) after the monochromator |
Radiation | Monochromator: Double-Crystal Si 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 107020 / Num. obs: 101570 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 24.3 Å2 / Limit h max: 78 / Limit h min: -84 / Limit k max: 42 / Limit k min: -84 / Limit l max: 57 / Limit l min: 0 / Observed criterion F max: 408469.96 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.339 / % possible all: 94.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 287321 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 94.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Armadillo repeat domain of murine beta-catenin, PDB code 2bct Resolution: 2→100 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.3 / Data cutoff high rms absF: 10000 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 59.3926 Å2 / ksol: 0.367974 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.29 Å2 / Biso mean: 47.05 Å2 / Biso min: 14.13 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→100 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: protein_rep.param | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5.5 % / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.328 |