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Yorodumi- PDB-1t08: Crystal structure of beta-catenin/ICAT helical domain/unphosphory... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t08 | ||||||
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Title | Crystal structure of beta-catenin/ICAT helical domain/unphosphorylated APC R3 | ||||||
Components |
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Keywords | cell adhesion/cell cycle / beta-catenin / Wnt signal / APC / 20mer repeat / Wnt signaling / cell adhesion-cell cycle COMPLEX | ||||||
Function / homology | Function and homology information regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / negative regulation of mesenchymal cell proliferation / APC truncation mutants are not K63 polyubiquitinated / armadillo repeat domain binding / 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 ...regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / negative regulation of mesenchymal cell proliferation / APC truncation mutants are not K63 polyubiquitinated / armadillo repeat domain binding / 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 microtubule-based movement / 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 / negative regulation of cell cycle G1/S phase transition / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / 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 / gamma-catenin binding / embryonic foregut morphogenesis / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / 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 / mesenchymal cell proliferation involved in lung development / detection of muscle stretch / smooth muscle cell differentiation / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / presynaptic active zone cytoplasmic component / positive regulation of protein localization to centrosome / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Germ layer formation at gastrulation / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / pattern specification process / bicellular tight junction assembly / embryonic brain development / epithelial cell differentiation involved in prostate gland development / Formation of definitive endoderm / protein kinase regulator activity / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of microtubule depolymerization / negative regulation of cyclin-dependent protein serine/threonine kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ha, N.-C. / Tonozuka, T. / Stamos, J.L. / 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. / Choi, H.J. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t08.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t08.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 1t08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/1t08 ftp://data.pdbj.org/pub/pdb/validation_reports/t0/1t08 | HTTPS FTP |
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-Related structure data
Related structure data | 1v18C 1m1eS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 56583.680 Da / Num. of mol.: 1 / Fragment: armadillo repeat (RESIDUES 146-664) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1,CTNNB / Plasmid: pPROEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35222 |
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#2: Protein/peptide | Mass: 5239.055 Da / Num. of mol.: 1 / Fragment: helical domain (RESIDUES 8-53) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNBIP1,ICAT / Plasmid: pPROEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NSA3 |
#3: Protein/peptide | Mass: 1633.688 Da / Num. of mol.: 1 / Fragment: repeat 3 (RESIDUES 1484-1498) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APC,DP2.5 / Plasmid: pGEXTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25054 |
#4: 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: 3.07 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 297 K / Method: evaporation / pH: 6.5 Details: PEG3400, Potassium phosphate, pH 6.5, EVAPORATION, temperature 297K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2003 | ||||||||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→100 Å / Num. all: 47853 / Num. obs: 47853 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.67 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.2 | ||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.16 / Num. unique all: 4230 / Rsym value: 0.296 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M1E Resolution: 2.1→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 465671.86 / 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: 45.2511 Å2 / ksol: 0.365862 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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