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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


negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / regulation of protein export from nucleus / superior temporal gyrus development / cellular response to interleukin-3 / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process ...negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / regulation of protein export from nucleus / superior temporal gyrus development / cellular response to interleukin-3 / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / beta-arrestin-dependent dopamine receptor signaling pathway / negative regulation of dopaminergic neuron differentiation / positive regulation of protein localization to centrosome / maintenance of cell polarity / positive regulation of cilium assembly / regulation of long-term synaptic potentiation / heart valve development / tau-protein kinase / CRMPs in Sema3A signaling / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / 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 / negative regulation of TOR signaling / positive regulation of cell-matrix adhesion / Wnt signalosome / regulation of microtubule-based process / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of axon extension / positive regulation of protein binding / regulation of neuron projection development / negative regulation of protein localization to nucleus / Maturation of nucleoprotein / glycogen metabolic process / ER overload response / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / regulation of axonogenesis / establishment of cell polarity / regulation of dendrite morphogenesis / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / canonical Wnt signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / dynactin binding / epithelial to mesenchymal transition / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / extrinsic apoptotic signaling pathway / NF-kappaB binding / negative regulation of protein-containing complex assembly / cellular response to retinoic acid / regulation of cellular response to heat / positive regulation of protein export from nucleus / positive regulation of type I interferon production / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of autophagy / negative regulation of cell migration / response to endoplasmic reticulum stress / excitatory postsynaptic potential / positive regulation of protein ubiquitination / hippocampus development / mitochondrion organization / positive regulation of cell differentiation / circadian rhythm / negative regulation of canonical Wnt signaling pathway / Ubiquitin-dependent degradation of Cyclin D / regulation of microtubule cytoskeleton organization / Wnt signaling pathway / positive regulation of protein-containing complex assembly / peptidyl-serine phosphorylation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / tau protein binding / insulin receptor signaling pathway / neuron projection development / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / positive regulation of protein catabolic process / kinase activity
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 (eV)
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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