|Entry||Database: PDB / ID: 4nm0|
|Title||Crystal structure of peptide inhibitor-free GSK-3/Axin complex|
|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 / genomic imprinting / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of canonical Wnt signaling pathway involved in osteoblast differentiation / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development ...armadillo repeat domain binding / head development / genomic imprinting / cell development / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of canonical Wnt signaling pathway involved in osteoblast differentiation / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / axial mesoderm formation / dorsal/ventral axis specification / positive regulation of protein localization to cilium / superior temporal gyrus development / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / beta-catenin destruction complex disassembly / positive regulation of protein localization to centrosome / maintenance of cell polarity / positive regulation of mitochondrion organization / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / I-SMAD binding / 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 / negative regulation of protein acetylation / tau-protein kinase / beta-catenin destruction complex / 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 / CRMPs in Sema3A signaling / positive regulation of ubiquitin-dependent protein catabolic process / Wnt signalosome / cellular response to interleukin-3 / Maturation of nucleoprotein / glycogen metabolic process / Disassembly of the destruction complex and recruitment of AXIN to the membrane / dopamine receptor signaling pathway / regulation of long-term synaptic potentiation / negative regulation of transcription elongation by RNA polymerase II / Maturation of nucleoprotein / regulation of neuron projection development / AKT phosphorylates targets in the cytosol / signaling adaptor activity / negative regulation of protein metabolic process / negative regulation of protein localization to nucleus / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / nucleocytoplasmic transport / negative regulation of phosphoprotein phosphatase activity / dynactin binding / negative regulation of fat cell differentiation / regulation of axon extension / regulation of dendrite morphogenesis / tau-protein kinase activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of axonogenesis / ER overload response / positive regulation of transforming growth factor beta receptor signaling pathway / canonical Wnt signaling pathway / positive regulation of ubiquitin-protein transferase activity / Constitutive Signaling by AKT1 E17K in Cancer / R-SMAD binding / lateral plasma membrane / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / SMAD binding / negative regulation of protein-containing complex assembly / regulation of cellular response to heat / protein kinase A catalytic subunit binding / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / NF-kappaB binding / activation of protein kinase activity / positive regulation of protein kinase activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / cellular response to retinoic acid / establishment of cell polarity / excitatory postsynaptic potential / extrinsic apoptotic signaling pathway in absence of ligand / hippocampus development / presynaptic modulation of chemical synaptic transmission / positive regulation of protein ubiquitination / positive regulation of protein export from nucleus / extrinsic apoptotic signaling pathway / positive regulation of peptidyl-threonine phosphorylation / cell periphery / Ubiquitin-dependent degradation of Cyclin D / TCF dependent signaling in response to WNT / positive regulation of JUN kinase activity
Similarity search - Function
Axin beta-catenin binding / Axin-1 / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1 / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Glycogen synthase kinase-3 beta / Glycogen synthase kinase 3, catalytic domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
|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.
|Structure viewer||Molecule: |
Downloads & links
A: Glycogen synthase kinase-3 beta
-Protein / Protein/peptide , 2 types, 2 molecules A
|#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
|#4: Chemical||#5: Chemical|| ChemComp-ADP / ||#6: Chemical|| ChemComp-DTT / ||#7: Chemical|| ChemComp-CL / ||#8: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|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
|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|
Diffraction-ID: 1 / Rejects: 0
|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|
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