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- PDB-6ae3: Crystal structure of GSK3beta complexed with Morin -

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Basic information

Entry
Database: PDB / ID: 6ae3
TitleCrystal structure of GSK3beta complexed with Morin
ComponentsGlycogen synthase kinase-3 beta
KeywordsSIGNALING PROTEIN / Kinase / Flavonoid
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Transcriptional and post-translational regulation of MITF-M expression and activity ...Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / B-WICH complex positively regulates rRNA expression / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / re-entry into mitotic cell cycle / Disassembly of the destruction complex and recruitment of AXIN to the membrane / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cardiac muscle cell differentiation / myotube differentiation / Degradation of beta-catenin by the destruction complex / protein localization to microtubule / negative regulation of cardiac muscle hypertrophy / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / GLI3 is processed to GLI3R by the proteasome / positive regulation of stem cell differentiation / negative regulation of TORC2 signaling / autosome genomic imprinting / positive regulation of cilium assembly / beta-catenin destruction complex / meiosis I / tau-protein kinase / regulation of microtubule-based process / myoblast fusion / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-3 / axon extension / phosphorylation / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / meiotic spindle / negative regulation of calcineurin-NFAT signaling cascade / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / cellular response to glucocorticoid stimulus / cellular response to hepatocyte growth factor stimulus / glycogen metabolic process / ER overload response / regulation of neuron projection development / dynein complex binding / fat cell differentiation / epithelial to mesenchymal transition / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / canonical Wnt signaling pathway / positive regulation of axon extension / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cytoskeleton organization / positive regulation of autophagy / positive regulation of substrate adhesion-dependent cell spreading / axonogenesis / protein export from nucleus / lipopolysaccharide-mediated signaling pathway / dendritic shaft / animal organ morphogenesis / positive regulation of protein export from nucleus / stem cell differentiation / regulation of cell growth / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of canonical Wnt signaling pathway / regulation of circadian rhythm / beta-catenin binding / Wnt signaling pathway / circadian rhythm / neuron projection development / peptidyl-serine phosphorylation / p53 binding / kinase activity / insulin receptor signaling pathway / cell migration / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / growth cone / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / intracellular signal transduction / protein phosphorylation / ribonucleoprotein complex / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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
Chem-MRI / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKim, K.L. / Cha, J.S. / Kim, J.S. / Ahn, J.S. / Ha, N.C. / Cho, H.S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of GSK3 beta in complex with the flavonoid, morin
Authors: Kim, K. / Cha, J.S. / Kim, J.S. / Ahn, J. / Ha, N.C. / Cho, H.S.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
C: Glycogen synthase kinase-3 beta
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,36210
Polymers187,3894
Non-polymers9736
Water7,602422
1
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4836
Polymers93,6942
Non-polymers7894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycogen synthase kinase-3 beta
D: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8794
Polymers93,6942
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.588, 134.360, 100.393
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 46847.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Tyrosine 217 is phosphorylated. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsk3b / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WV60, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MRI / 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one / Morin


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Sodium Citrate (pH6.5), 18%(v/v) PEG 4000, 5%(v/v) 2-propanol

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Data collection

DiffractionMean temperature: 83 K / Ambient temp details: 83
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 93509 / % possible obs: 97.8 % / Redundancy: 6 % / Net I/σ(I): 38.17
Reflection shellResolution: 2.14→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.14 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22626 4608 4.9 %RANDOM
Rwork0.1906 ---
obs0.19236 88879 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å21.2 Å2
2--0.74 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.14→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10463 0 68 422 10953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01410789
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179620
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.67614754
X-RAY DIFFRACTIONr_angle_other_deg0.9691.63222419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19951339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2221.394495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.678151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5551567
X-RAY DIFFRACTIONr_chiral_restr0.0760.21460
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021978
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9344.8275412
X-RAY DIFFRACTIONr_mcbond_other3.9324.8265411
X-RAY DIFFRACTIONr_mcangle_it5.6067.2096731
X-RAY DIFFRACTIONr_mcangle_other5.6067.216732
X-RAY DIFFRACTIONr_scbond_it4.1714.9585377
X-RAY DIFFRACTIONr_scbond_other4.1684.9585377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0787.3658024
X-RAY DIFFRACTIONr_long_range_B_refined9.04388.81644513
X-RAY DIFFRACTIONr_long_range_B_other9.03588.89344226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 309 -
Rwork0.268 6267 -
obs--93.37 %

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