+Open data
-Basic information
Entry | Database: PDB / ID: 8vmg | ||||||||||||
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Title | Crystal structure of GSK-3 26-383 bound to Axin 383-435 | ||||||||||||
Components |
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Keywords | TRANSFERASE/SIGNALING PROTEIN / GSK-3 / kinase / TRANSFERASE-SIGNALING PROTEIN complex | ||||||||||||
Function / homology | Function and homology information hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / membrane-bounded organelle ...hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / membrane-bounded organelle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of synaptic assembly at neuromuscular junction / positive regulation of osteoclast proliferation / armadillo repeat domain binding / Transcriptional and post-translational regulation of MITF-M expression and activity / myotube differentiation / cell growth involved in cardiac muscle cell development / negative regulation of neuron migration / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / positive regulation of cardiac muscle cell differentiation / negative regulation of dendrite morphogenesis / head development / Degradation of beta-catenin by the destruction complex / cell development / protein localization to microtubule / negative regulation of cardiac muscle hypertrophy / neuron projection organization / dorsal/ventral axis specification / positive regulation of stem cell differentiation / axial mesoderm formation / negative regulation of dendrite development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / GLI3 is processed to GLI3R by the proteasome / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / autosome genomic imprinting / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / positive regulation of cilium assembly / negative regulation of protein acetylation / bone remodeling / post-anal tail morphogenesis / 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 / positive regulation of ubiquitin-dependent protein catabolic process / myoblast fusion / epigenetic programming in the zygotic pronuclei / regulation of protein export from nucleus / regulation of microtubule-based process / regulation of modification of postsynaptic structure / 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 / positive regulation of osteoclast differentiation / I-SMAD binding / axon extension / cellular response to interleukin-3 / meiotic spindle / negative regulation of TOR signaling / Wnt signalosome / negative regulation of protein localization to nucleus / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cellular response to glucocorticoid stimulus / negative regulation of protein metabolic process / nucleocytoplasmic transport / positive regulation of mitochondrial membrane potential / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of epithelial to mesenchymal transition / regulation of osteoblast differentiation / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / establishment or maintenance of cell polarity / glycogen metabolic process / positive regulation of DNA biosynthetic process / establishment of cell polarity / cellular response to hepatocyte growth factor stimulus / tau-protein kinase activity / regulation of axonogenesis / regulation of dendrite morphogenesis / response to zinc ion / activation of protein kinase activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / negative regulation of fat cell differentiation / dynein complex binding / hepatocyte apoptotic process / regulation of neuron projection development / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of osteoblast proliferation / negative regulation of transcription elongation by RNA polymerase II Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||||||||
Authors | Enos, M.D. / Gavagan, M. / Jameson, N. / Zalatan, J.G. / Weis, W.I. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci.Signal. / Year: 2024 Title: Structural and functional effects of phosphopriming and scaffolding in the kinase GSK-3 beta. Authors: Enos, M.D. / Gavagan, M. / Jameson, N. / Zalatan, J.G. / 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 | 8vmg.cif.gz | 414.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vmg.ent.gz | 286.5 KB | Display | PDB format |
PDBx/mmJSON format | 8vmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vmg_validation.pdf.gz | 882 KB | Display | wwPDB validaton report |
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Full document | 8vmg_full_validation.pdf.gz | 896.5 KB | Display | |
Data in XML | 8vmg_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 8vmg_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/8vmg ftp://data.pdbj.org/pub/pdb/validation_reports/vm/8vmg | HTTPS FTP |
-Related structure data
Related structure data | 8vmeC 8vmfC 4nm0S 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 41538.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsk3b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase #2: Protein | Mass: 6657.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15169 |
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-Non-polymers , 9 types, 236 molecules
#3: Chemical | ChemComp-ADP / | ||||||||||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NO3 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-MG / | #9: Chemical | ChemComp-CL / #10: Chemical | ChemComp-MES / | #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 4.36 Å3/Da / Density % sol: 71.8 % / Description: Hexagonal bipyramidal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→39.76 Å / Num. obs: 63244 / % possible obs: 99.9 % / Redundancy: 41.1 % / Biso Wilson estimate: 66.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.035 / Rrim(I) all: 0.225 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 42.2 % / Rmerge(I) obs: 8.11 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4331 / CC1/2: 0.414 / Rpim(I) all: 1.258 / Rrim(I) all: 8.208 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NM0 Resolution: 2.45→39.76 Å / SU ML: 0.4315 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6462 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→39.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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