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- PDB-1jpp: The Structure of a beta-Catenin Binding Repeat from Adenomatous P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jpp | ||||||
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Title | The Structure of a beta-Catenin Binding Repeat from Adenomatous Polyposis Coli (APC) in Complex with beta-Catenin | ||||||
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![]() | CELL ADHESION / Disease mutation / Anti-oncogene | ||||||
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 / APC truncation mutants are not K63 polyubiquitinated / 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 / APC truncation mutants are not K63 polyubiquitinated / 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 / regulation of microtubule-based movement / 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 / Ca2+ pathway / central nervous system vasculogenesis / animal organ development / 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 / negative regulation of cell cycle G1/S phase transition / 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 / 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 / gamma-catenin binding / 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 / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / 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 / regulation of osteoclast differentiation / 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 / presynaptic active zone cytoplasmic component / smooth muscle cell differentiation / cell projection membrane / positive regulation of protein localization to centrosome / histone methyltransferase binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spink, K.E. / Fridman, S.G. / Weis, W.I. | ||||||
![]() | ![]() Title: Molecular mechanisms of beta-catenin recognition by adenomatous polyposis coli revealed by the structure of an APC-beta-catenin complex. Authors: Eklof Spink, K. / Fridman, S.G. / Weis, W.I. #1: ![]() 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. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.5 KB | Display | ![]() |
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PDB format | ![]() | 161.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 473.1 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g3jS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58844.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1786.911 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: P25054 #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.23 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, sodium potassium phosphate, sodium chloride, DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2001 |
Radiation | Monochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→28.3 Å / Num. all: 21958 / Num. obs: 19916 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 1.47 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 1.39 % / Rmerge(I) obs: 0.242 / Num. unique all: 1937 / % possible all: 87.8 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 87.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1G3J Resolution: 3.1→28.27 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1211274.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.503 Å2 / ksol: 0.320417 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→28.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.394 / % reflection Rfree: 6.2 % / Rfactor Rwork: 0.347 |