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Yorodumi- PDB-8vme: Crystal structure of the GSK-3/Axin complex bound to a phosphoryl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vme | ||||||||||||
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Title | Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide | ||||||||||||
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 / TCF dependent signaling in response to WNT / armadillo repeat domain binding / Degradation of AXIN / Transcriptional and post-translational regulation of MITF-M expression and activity / myotube differentiation / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / oviduct development / 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 / cell growth involved in cardiac muscle cell development / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / central nervous system vasculogenesis / astrocyte-dopaminergic neuron signaling / negative regulation of neuron migration / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / positive regulation of cardiac muscle cell differentiation / negative regulation of mitotic cell cycle, embryonic / negative regulation of dendrite morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / head development / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / embryonic axis specification / Specification of the neural plate border / cell development / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / protein localization to microtubule / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / negative regulation of cardiac muscle hypertrophy / neuron projection organization / acinar cell differentiation / dorsal/ventral axis specification / positive regulation of stem cell differentiation / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / positive regulation of myoblast proliferation / axial mesoderm formation / hair follicle placode formation / fungiform papilla formation / sympathetic ganglion development / negative regulation of dendrite development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / embryonic foregut morphogenesis / lung epithelial cell differentiation / hindbrain development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of skeletal muscle tissue development / GLI3 is processed to GLI3R by the proteasome / cellular response to indole-3-methanol / regulation of calcium ion import / regulation of protein localization to cell surface / hair cell differentiation / negative regulation of dopaminergic neuron differentiation Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 8vme.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vme.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 8vme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vme_validation.pdf.gz | 778.7 KB | Display | wwPDB validaton report |
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Full document | 8vme_full_validation.pdf.gz | 783 KB | Display | |
Data in XML | 8vme_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8vme_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/8vme ftp://data.pdbj.org/pub/pdb/validation_reports/vm/8vme | HTTPS FTP |
-Related structure data
Related structure data | 8vmfC 8vmgC 4nm7S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41666.824 Da / Num. of mol.: 1 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 |
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-Protein/peptide , 2 types, 2 molecules BC
#2: Protein/peptide | Mass: 2738.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Axin1, Axin, Fu / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O35625 |
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#3: Protein/peptide | Mass: 2911.952 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35222 |
-Non-polymers , 5 types, 184 molecules
#4: Chemical | ChemComp-ADP / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-NA / | #8: 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: 2.93 Å3/Da / Density % sol: 58.01 % / Description: Flat plates |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 Details: 10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 200 uM ATP, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97949 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.47 Å / Num. obs: 26090 / % possible obs: 99.9 % / Redundancy: 35.5 % / Biso Wilson estimate: 59.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.026 / Rrim(I) all: 0.154 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 21.8 % / Rmerge(I) obs: 5.635 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2435 / CC1/2: 0.399 / Rpim(I) all: 1.201 / Rrim(I) all: 5.768 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NM7 Resolution: 2.3→39.47 Å / SU ML: 0.3359 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0862 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: 72.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.47 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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