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Yorodumi- PDB-4nm5: Crystal structure of GSK-3/Axin complex bound to phosphorylated W... -
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-Basic information
Entry | Database: PDB / ID: 4nm5 | ||||||
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Title | Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif | ||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / phosphorylated Wnt receptor LRP6 c-motif / TRANSFERASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information regulation of cellular component organization / Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / head development / cell development ...regulation of cellular component organization / Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / head development / cell development / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / negative regulation of smooth muscle cell apoptotic process / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / toxin transmembrane transporter activity / negative regulation of mesenchymal stem cell differentiation / 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 / Wnt-protein binding / midbrain dopaminergic neuron differentiation / cellular response to cholesterol / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / beta-catenin destruction complex disassembly / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / positive regulation of ubiquitin-dependent protein catabolic process / post-anal tail morphogenesis / negative regulation of protein acetylation / negative regulation of protein serine/threonine kinase activity / epigenetic programming in the zygotic pronuclei / tau-protein kinase / 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 / dopaminergic neuron differentiation / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / frizzled binding / 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 / neural crest cell differentiation / negative regulation of protein metabolic process / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of protein localization to nucleus / glycogen metabolic process / 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 / tau-protein kinase activity / regulation of axonogenesis / establishment of cell polarity / 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 developmental process / negative regulation of transcription elongation by RNA polymerase II / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / activation of protein kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / R-SMAD binding / canonical Wnt signaling pathway / ubiquitin ligase-substrate adaptor activity / NF-kappaB binding / Regulation of HSF1-mediated heat shock response / lateral plasma membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Stamos, J.L. / Chu, M.L.-H. / Enos, M.D. / Shah, N. / Weis, W.I. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6. Authors: Stamos, J.L. / Chu, M.L. / Enos, M.D. / Shah, N. / 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 | 4nm5.cif.gz | 178 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nm5.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nm5 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nm5 | HTTPS FTP |
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-Related structure data
Related structure data | 4nm0C 4nm3C 4nm7SC 4nu1C C: citing same article (ref.) 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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2 |
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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: 42857.160 Da / Num. of mol.: 1 / Fragment: Residues 13-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B, hCG_1818062 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL References: UniProt: Q6FI27, UniProt: P49841*PLUS, tau-protein kinase |
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-Protein/peptide , 2 types, 2 molecules BC
#2: Protein/peptide | Mass: 2738.144 Da / Num. of mol.: 1 / Fragment: Residues 383-402 Source method: isolated from a genetically manipulated source Details: Modified pGEX-KG / Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O15169 |
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#3: Protein/peptide | Mass: 1060.141 Da / Num. of mol.: 1 / Fragment: Residues 1568-1575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O75581*PLUS |
-Non-polymers , 5 types, 129 molecules
#4: Chemical | ChemComp-ADP / | ||||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-CL / | #8: 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: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 Details: 10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2013 | |||||||||||||||||||||
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→39.24 Å / Num. all: 25689 / Num. obs: 25685 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 56.74 Å2 / Rsym value: 0.141 / Net I/σ(I): 18.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NM7 Resolution: 2.3→39.237 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8334 / SU ML: 0.31 / σ(F): 1.91 / Phase error: 22.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 173.4 Å2 / Biso mean: 70.3538 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.237 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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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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