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- PDB-1i09: STRUCTURE OF GLYCOGEN SYNTHASE KINASE-3 (GSK3B) -

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Basic information

Entry
Database: PDB / ID: 1i09
TitleSTRUCTURE OF GLYCOGEN SYNTHASE KINASE-3 (GSK3B)
ComponentsGLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE / kinase / beta barrel
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / beta-catenin destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the 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 / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-3 / Maturation of nucleoprotein / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / glycogen metabolic process / ER overload response / establishment of cell polarity / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / NF-kappaB binding / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / positive regulation of protein binding / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / Transcriptional and post-translational regulation of MITF-M expression and activity / presynaptic modulation of chemical synaptic transmission / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / excitatory postsynaptic potential / mitochondrion organization / hippocampus development / positive regulation of cell differentiation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / circadian rhythm / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / beta-catenin binding / peptidyl-serine phosphorylation / B-WICH complex positively regulates rRNA expression / tau protein binding / Wnt signaling pathway / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of protein catabolic process / p53 binding / kinase activity / insulin receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of neuron apoptotic process
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
PHOSPHATE ION / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTer Haar, E. / Coll, J.T. / Jain, J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of GSK3beta reveals a primed phosphorylation mechanism.
Authors: ter Haar, E. / Coll, J.T. / Austen, D.A. / Hsiao, H.M. / Swenson, L. / Jain, J.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors have analyzed the GSK3b sequences (expressed sequence tags databases) ...SEQUENCE The authors have analyzed the GSK3b sequences (expressed sequence tags databases) carefully and came to the conclusion that there is an error in P49841 sequence. HIS 350 should be a LEU. It is definitely a LEU in crystal structure sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9826
Polymers93,6022
Non-polymers3804
Water82946
1
A: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9913
Polymers46,8011
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9913
Polymers46,8011
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.272, 86.725, 177.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / GSK-3 BETA / GSK3B


Mass: 46801.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: P49841, EC: 2.7.1.37
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: PEG 3350 Na/K Phosphate DTT, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
215 %(v/v)PEG33501reservoir
350 mMsodium potassium phosphate1reservoirpH4.1
410 mMdithiothreitol1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→48.31 Å / Num. all: 35382 / Num. obs: 34747 / % possible obs: 96 % / Redundancy: 4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.322 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 34993 / % possible obs: 98.9 % / Num. measured all: 251279 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNXrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 3146 random
Rwork0.242 --
all-36194 -
obs-34747 -
Refinement stepCycle: LAST / Resolution: 2.7→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 20 46 5304
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.352 467 -
Rwork0.325 --
obs-5051 92.8 %
Software
*PLUS
Name: CNX / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 48.3 Å / σ(F): 0 / % reflection Rfree: 9.1 % / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.352 / Rfactor Rwork: 0.325

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