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- PDB-6gn1: Crystal Structure of Glycogen synthase kinase-3 beta (GSK3B) in C... -

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Basic information

Entry
Database: PDB / ID: 6gn1
TitleCrystal Structure of Glycogen synthase kinase-3 beta (GSK3B) in Complex with PIK-75
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / Glycogen synthase kinase-3 beta / PIK-75 / halogen bond / inhibitor
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 / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / 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 / 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 / beta-catenin destruction complex / tau-protein kinase / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / 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 / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / 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 / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of protein-containing complex assembly / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / negative regulation of canonical Wnt signaling pathway / tau protein binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / positive regulation of GTPase activity / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / presynapse / insulin receptor signaling pathway / positive regulation of protein binding / kinase activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 ...Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-F4N / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTesch, R. / Becker, C. / Mueller, M.P. / Sant'Anna, C.M.R. / Fraga, C.A.M. / Rauh, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchBMBF 01GS08104 Germany
German Federal Ministry for Education and Research01ZX1303C Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: An Unusual Intramolecular Halogen Bond Guides Conformational Selection.
Authors: Tesch, R. / Becker, C. / Muller, M.P. / Beck, M.E. / Quambusch, L. / Getlik, M. / Lategahn, J. / Uhlenbrock, N. / Costa, F.N. / Poleto, M.D. / Pinheiro, P.S.M. / Rodrigues, D.A. / Sant'Anna, ...Authors: Tesch, R. / Becker, C. / Muller, M.P. / Beck, M.E. / Quambusch, L. / Getlik, M. / Lategahn, J. / Uhlenbrock, N. / Costa, F.N. / Poleto, M.D. / Pinheiro, P.S.M. / Rodrigues, D.A. / Sant'Anna, C.M.R. / Ferreira, F.F. / Verli, H. / Fraga, C.A.M. / Rauh, D.
History
DepositionMay 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Glycogen synthase kinase-3 beta
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3176
Polymers83,3412
Non-polymers9754
Water1,964109
1
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1583
Polymers41,6711
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1583
Polymers41,6711
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.630, 119.500, 67.480
Angle α, β, γ (deg.)90.00, 102.49, 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: 41670.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-F4N / ~{N}-[(~{E})-(6-bromanylimidazo[1,2-a]pyridin-3-yl)methylideneamino]-~{N},2-dimethyl-5-nitro-benzenesulfonamide


Mass: 452.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14BrN5O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: reservoir 0,1 M HEPES pH 7.0, 22% v/v PEG 8000, 8% ethylenglycol, 5mg/ml GSK3B (in 25 mM TRIS, 250 mM NaCl, 10 % Glycerol, pH 8), 1ul reservoir + 1ul protein solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.91883 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91883 Å / Relative weight: 1
ReflectionResolution: 2.6→48.21 Å / Num. obs: 32218 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.13 / Net I/σ(I): 11.99
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 3475 / CC1/2: 0.804 / Rrim(I) all: 0.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J1R

4j1r


Resolution: 2.6→44.304 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2589 1611 5 %
Rwork0.2217 --
obs0.2236 32189 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 56 109 5613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085640
X-RAY DIFFRACTIONf_angle_d1.087684
X-RAY DIFFRACTIONf_dihedral_angle_d10.4973404
X-RAY DIFFRACTIONf_chiral_restr0.071862
X-RAY DIFFRACTIONf_plane_restr0.007980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.35121330.32542525X-RAY DIFFRACTION100
2.6765-2.76290.35761330.29582524X-RAY DIFFRACTION100
2.7629-2.86160.32851340.26992551X-RAY DIFFRACTION100
2.8616-2.97620.28111340.25672540X-RAY DIFFRACTION100
2.9762-3.11160.30851350.26642558X-RAY DIFFRACTION100
3.1116-3.27560.35931330.27312521X-RAY DIFFRACTION100
3.2756-3.48070.28641340.23522544X-RAY DIFFRACTION100
3.4807-3.74940.27931340.22372558X-RAY DIFFRACTION100
3.7494-4.12640.26281340.21032528X-RAY DIFFRACTION100
4.1264-4.72290.22091350.18222574X-RAY DIFFRACTION100
4.7229-5.94810.17661350.18612554X-RAY DIFFRACTION100
5.9481-44.30990.22911370.20582601X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7660.0684-0.20772.7759-0.92053.01670.1103-0.04180.28990.0649-0.124-0.0813-0.11460.23830.02220.2238-0.06540.02610.5389-0.06120.3297-11.35438.104-29.5294
23.19170.8940.17073.25970.1442.1860.0153-0.2317-0.07940.0669-0.0596-0.04750.3303-0.13530.03080.25840.04460.03310.51630.0870.243111.4793-12.7536-47.7833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 36:383)
2X-RAY DIFFRACTION2(chain A and resseq 36:383)

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