+Open data
-Basic information
Entry | Database: PDB / ID: 4nm0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of peptide inhibitor-free GSK-3/Axin complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / TRANSFERASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information armadillo repeat domain binding / head development / cell development / 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 ...armadillo repeat domain binding / head development / cell development / 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 / 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 / post-anal tail morphogenesis / 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 / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / tau-protein kinase / positive regulation of ubiquitin-dependent protein catabolic process / 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 / I-SMAD binding / 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 / 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 / dopamine receptor signaling pathway / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / negative regulation of fat cell differentiation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / activation of protein kinase activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / signaling adaptor activity / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cytoplasmic microtubule organization / 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 / excitatory postsynaptic potential / negative regulation of insulin receptor signaling pathway / positive regulation of protein export from nucleus / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / Ubiquitin-dependent degradation of Cyclin D / cell periphery / hippocampus development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chu, M.L.-H. / Stamos, J.L. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nm0.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nm0.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/4nm0 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/4nm0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4nm3C 4nm5C 4nm7SC 4nu1C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 44180.625 Da / Num. of mol.: 1 / Fragment: Residues 1-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase |
---|---|
#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.) Homo sapiens (human) / Gene: AXIN, AXIN1 / Plasmid: Modified pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O15169 |
-Non-polymers , 6 types, 174 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-DTT / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % / Mosaicity: 0.18 ° |
---|---|
Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 Details: 10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 20mM MgCl2, 400uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å | ||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→39.05 Å / Num. obs: 20069 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Rrim(I) all: 0.112 / Rsym value: 0.106 / Net I/σ(I): 18.4 / Num. measured all: 192347 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NM7 Resolution: 2.5→39.048 Å / SU ML: 0.34 / σ(F): 1.91 / Phase error: 25.87 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.048 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|