[English] 日本語
Yorodumi- PDB-1v18: The crystal structure of beta-catenin armadillo repeat complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v18 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of beta-catenin armadillo repeat complexed with a phosphorylated APC 20mer repeat. | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / SIGNALLING COMPLEX / WNT SIGNAL / BETA-CATENIN DEGRADATION COMPLEX / CELL ADHESION / TRANSCRIPTION / TRANSCRIPTION REGULATION | ||||||
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 / 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 / regulation of epithelial cell differentiation / Schwann cell proliferation / animal organ development / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / Degradation of beta-catenin by the destruction complex / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / negative regulation of cell cycle G1/S phase transition / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / positive regulation of fibroblast growth factor receptor signaling pathway / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / 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 / sympathetic ganglion development / establishment of blood-retinal barrier / 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 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 / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / presynaptic active zone cytoplasmic component / smooth muscle cell differentiation / histone methyltransferase binding / cell projection membrane / positive regulation of protein localization to centrosome Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ha, N.-C. / Weis, W.I. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Mechanism of Phosphorylation-Dependent Binding of Apc to Beta-Catenin and its Role in Beta-Catenin Degradation Authors: Ha, N.-C. / Tonozuka, T. / Stamos, J.L. / Weis, W.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v18.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v18.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 1v18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/1v18 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/1v18 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1t08C 1i7wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 58844.117 Da / Num. of mol.: 1 Fragment: ARMADILLO REPEAT, REPEAT 3 OF APC, RESIDUES 134-671 Source method: isolated from a genetically manipulated source Details: 134-671 OF BETA-CATENIN AND 1484-1528 OF HUMAN APC(ADENOMATOUS POLYPOSIS COLI) PHOSPHORYLATED BY CK1 AND GSK-3BETA Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q02248 |
---|---|
#2: Protein/peptide | Mass: 5414.617 Da / Num. of mol.: 1 / Fragment: RESIDUES 1482-1528 Source method: isolated from a genetically manipulated source Details: 134-671 OF BETA-CATENIN AND 1484-1528 OF HUMAN APC(ADENOMATOUS POLYPOSIS COLI) PHOSPHORYLATED BY CK1 AND GSK-3BETA Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25054 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.76 % |
---|---|
Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 31262 / % possible obs: 97.4 % / Redundancy: 7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 37 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.6 / % possible all: 85.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I7W Resolution: 2.1→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.5715 Å2 / ksol: 0.376423 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|