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- PDB-1p22: Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p22 | ||||||
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Title | Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase | ||||||
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![]() | SIGNALING PROTEIN / Ubiquitination / degradation | ||||||
Function / homology | ![]() protein phosphorylated amino acid 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 ...protein phosphorylated amino acid 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 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 / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / F-box domain binding / 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 / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / 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 / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of skeletal muscle tissue development / PcG protein complex / cranial skeletal system development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / positive regulation of odontoblast differentiation / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / establishment of blood-brain barrier / Germ layer formation at gastrulation / negative regulation of oligodendrocyte differentiation / male genitalia development / fascia adherens / flotillin complex / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / epithelial cell differentiation involved in prostate gland development / Formation of definitive endoderm / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / embryonic brain development / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / beta-catenin destruction complex / oocyte development / ubiquitin ligase activator activity / adherens junction assembly / lung-associated mesenchyme development / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / Formation of axial mesoderm / positive regulation of circadian rhythm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, G. / Xu, G. / Schulman, B.A. / Jeffrey, P.D. / Harper, J.W. / Pavletich, N.P. | ||||||
![]() | ![]() Title: Structure of a beta-TrCP1-Skp1-beta-Catenin complex: destruction motif binding and lysine specificity of the SCFbeta-TrCP1 ubiquitin ligase Authors: Wu, G. / Xu, G. / Schulman, B.A. / Jeffrey, P.D. / Harper, J.W. / Pavletich, N.P. | ||||||
History |
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Remark 999 | an appropriate sequence database reference for Skp1, chain B, was not available at the time of processing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 93.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
#1: Protein | Mass: 49699.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 16590.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 2904.903 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.23 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2001 |
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→20 Å / Num. all: 17628 / Num. obs: 17628 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.04 |
Reflection shell | Resolution: 2.95→3.025 Å / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 52111 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 2.95 Å / Rmerge(I) obs: 0.43 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.95 Å / Lowest resolution: 3.025 Å / Rfactor Rfree: 0.511 / Rfactor Rwork: 0.433 / Num. reflection Rwork: 1201 |