+Open data
-Basic information
Entry | Database: PDB / ID: 7u2z | ||||||
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Title | Crystal structure of human GSK3B in complex with G12 | ||||||
Components | Glycogen synthase kinase-3 beta | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | Function and homology information regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / 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 / 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 / beta-catenin destruction complex / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / 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 / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / G protein-coupled dopamine receptor signaling pathway / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / glycogen metabolic process / ER overload response / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / NF-kappaB binding / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of autophagy / 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 / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / excitatory postsynaptic potential / positive regulation of protein export from nucleus / positive regulation of GTPase activity / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of protein-containing complex assembly / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / tau protein binding / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / positive regulation of neuron apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / presynapse / insulin receptor signaling pathway / negative regulation of neuron projection development / kinase activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Tripathi, S.K. / Balboni, B. / Giabbai, B. / Storici, P. / Girotto, S. / Cavalli, A. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Identification of Novel GSK-3 beta Hits Using Competitive Biophysical Assays. Authors: Balboni, B. / Tripathi, S.K. / Veronesi, M. / Russo, D. / Penna, I. / Giabbai, B. / Bandiera, T. / Storici, P. / Girotto, S. / Cavalli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u2z.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u2z.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 7u2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u2z_validation.pdf.gz | 1015.4 KB | Display | wwPDB validaton report |
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Full document | 7u2z_full_validation.pdf.gz | 1020.1 KB | Display | |
Data in XML | 7u2z_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 7u2z_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/7u2z ftp://data.pdbj.org/pub/pdb/validation_reports/u2/7u2z | HTTPS FTP |
-Related structure data
Related structure data | 7u31C 7u33C 7u36C 1i09S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39532.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG3350, Sodium Chloride, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→89.08 Å / Num. obs: 60774 / % possible obs: 95.6 % / Redundancy: 12.2 % / CC1/2: 0.993 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.21→2.26 Å / Redundancy: 11.4 % / Num. unique obs: 4107 / CC1/2: 0.36 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I09 Resolution: 2.21→89.07 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.061 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.7 Å2 / Biso mean: 54.117 Å2 / Biso min: 22.21 Å2
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Refinement step | Cycle: final / Resolution: 2.21→89.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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