[English] 日本語
![](img/lk-miru.gif)
- PDB-4nm7: Crystal structure of GSK-3/Axin complex bound to phosphorylated W... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4nm7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / primed substrate / Kinase / Axin / phosphorylated Wnt receptor LRP6 e-motif / TRANSFERASE-PEPTIDE complex | ||||||
Function / homology | ![]() 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 / toxin transmembrane transporter activity / low-density lipoprotein particle receptor activity / 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 / dorsal/ventral axis specification / negative regulation of type B pancreatic cell development / axial mesoderm formation / Wnt receptor activity / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / cellular response to cholesterol / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / midbrain dopaminergic neuron differentiation / : / Wnt-protein binding / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of protein acetylation / post-anal tail morphogenesis / negative regulation of protein serine/threonine kinase activity / 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 / epigenetic programming in the zygotic pronuclei / tau-protein kinase / positive regulation of ubiquitin-dependent protein catabolic process / dopaminergic neuron differentiation / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / 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 / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / neural crest cell differentiation / 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 / nucleocytoplasmic transport / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein metabolic process / 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 / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of fat cell differentiation / activation of protein kinase activity / ER overload response / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of developmental process / negative regulation of transcription elongation by RNA polymerase II / SMAD binding / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / dynactin binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / canonical Wnt signaling pathway Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Stamos, J.L. / Chu, M.L.-H. / Enos, M.D. / Shah, N. / Weis, W.I. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 139.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 803.5 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nm0C ![]() 4nm3C ![]() 4nm5C ![]() 4nu1C ![]() 1o9uS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
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.) ![]() ![]() ![]() References: UniProt: Q6FI27, UniProt: P49841*PLUS, tau-protein kinase |
---|
-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 Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#3: Protein/peptide | Mass: 1006.089 Da / Num. of mol.: 1 / Fragment: Residues 1603-1610 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 114 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ADP / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-DTT / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.57 % |
---|---|
Crystal grow | Temperature: 277 K / 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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 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→39.352 Å / Num. obs: 25932 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 60.05 Å2 / Rsym value: 0.136 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 18.2 % / Mean I/σ(I) obs: 0.9 / Rsym value: 4.307 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O9U Resolution: 2.3→39.35 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.37 / σ(F): 1.91 / Phase error: 24.14 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.35 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|