+Open data
-Basic information
Entry | Database: PDB / ID: 1o9u | ||||||
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Title | GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH AXIN PEPTIDE | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / KINASE / INSULIN PATHWAY / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / MULTIGENE FAMILY / PHOSPHORYLATION / DEVELOPMENTAL PROTEIN / ANTI-ONCOGENE / APOPTOSIS / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development ...armadillo repeat domain binding / head development / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / axial mesoderm formation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / post-anal tail morphogenesis / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / tau-protein kinase / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / I-SMAD binding / negative regulation of protein metabolic process / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nucleocytoplasmic transport / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / negative regulation of fat cell differentiation / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / regulation of neuron projection development / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / activation of protein kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / lateral plasma membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / signaling adaptor activity / positive regulation of autophagy / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / Ubiquitin-dependent degradation of Cyclin D / cell periphery / hippocampus development / positive regulation of protein-containing complex assembly Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Dajani, R. / Pearl, L.H. / Roe, S.M. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structural Basis for Recruitment of Glycogen Synthase Kinase 3Beta to the Axin-Apc Scaffold Complex Authors: Dajani, R. / Fraser, E. / Roe, S.M. / Yeo, M. / Good, V. / Thompson, V. / Dale, T.C. / Pearl, L.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9u.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9u.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9u ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9u | HTTPS FTP |
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-Related structure data
Related structure data | 1h8fS S: Starting model for refinement |
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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: 39622.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-384 Source method: isolated from a genetically manipulated source Details: PHOSPHOTYROSINE AT A216 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC HTA / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P49841, EC: 2.7.1.37 |
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#2: Protein/peptide | Mass: 2139.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 383-400 / Source method: obtained synthetically / Details: AXIN PEPTIDE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O15169 |
#3: Chemical | ChemComp-ADZ / |
#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: 2.7 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL ...Details: CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL PRECIPITANT (18% PEG4000, 150MM MGCL2, 100MM TRIS- HCL, PH 7.5) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9253 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9253 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24 Å / Num. obs: 22740 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.076 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.305 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 99.7 % / Redundancy: 3.9 % / Num. unique obs: 3252 / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H8F Resolution: 2.4→23.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2031993.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.15 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→23.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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