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- PDB-7z1g: Crystal structure of nonphosphorylated (Tyr216) GSK3b in complex ... -

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Basic information

Entry
Database: PDB / ID: 7z1g
TitleCrystal structure of nonphosphorylated (Tyr216) GSK3b in complex with CX-4945
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / Kinase / diabetes / kinase inhibitor
Function / homology
Function and homology information


regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / neuron projection organization / negative regulation of type B pancreatic cell development / superior temporal gyrus development / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of protein localization to cilium ...regulation of microtubule anchoring at centrosome / beta-catenin destruction complex disassembly / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / neuron projection organization / negative regulation of type B pancreatic cell development / superior temporal gyrus development / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / positive regulation of protein localization to centrosome / maintenance of cell polarity / 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 / CRMPs in Sema3A signaling / heart valve development / 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 / Maturation of nucleoprotein / cellular response to interleukin-3 / negative regulation of TOR signaling / Wnt signalosome / negative regulation of protein localization to nucleus / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of epithelial to mesenchymal transition / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / G protein-coupled dopamine receptor signaling pathway / regulation of axonogenesis / regulation of dendrite morphogenesis / tau-protein kinase activity / establishment of cell polarity / glycogen metabolic process / ER overload response / regulation of neuron projection development / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / NF-kappaB binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / canonical Wnt signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / presynaptic modulation of chemical synaptic transmission / positive regulation of GTPase activity / positive regulation of protein export from nucleus / excitatory postsynaptic potential / negative regulation of cell migration / positive regulation of protein ubiquitination / hippocampus development / Ubiquitin-dependent degradation of Cyclin D / mitochondrion organization / peptidyl-threonine phosphorylation / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / positive regulation of protein-containing complex assembly / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / 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 / beta-catenin binding / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / p53 binding / positive regulation of protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / insulin receptor signaling pathway / kinase activity
Similarity search - Function
: / Glycogen synthase kinase 3, catalytic domain / 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
Similarity search - Domain/homology
Chem-3NG / IMIDAZOLE / MALONATE ION / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGrygier, P. / Pustelny, K. / Dubin, G. / Czarna, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/E/NZ1/00467 Poland
National Center for Research and Development (Poland)PPN/PPO/2018/1/00046 Poland
CitationJournal: To Be Published
Title: Crystal structure of nonphosphorylated (Tyr216) GSK3b kinase in complex with CX-4945
Authors: Grygier, P. / Pustelny, K. / Golik, P. / Popowicz, G. / Dubin, G. / Czarna, A.
History
DepositionFeb 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,5039
Polymers41,5051
Non-polymers9988
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.812, 84.812, 195.968
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 41504.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, inhibitor*YM
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.23 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Sodium acetate trihydrate 0.1 M Imidazole pH 6.5, 0.2 M di-Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→44.18 Å / Num. obs: 17331 / % possible obs: 99.4 % / Redundancy: 9.9 % / Biso Wilson estimate: 73.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.046 / Rrim(I) all: 0.148 / Net I/σ(I): 14.9 / Num. measured all: 172129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-310.41.8682559624620.5440.5951.9641.599.6
9.01-44.187.80.02750246460.9990.010.0295198

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GN1

6gn1


Resolution: 2.85→42.42 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 850 4.91 %RANDOM
Rwork0.203 16445 --
obs0.2042 17295 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.2 Å2 / Biso mean: 79.6962 Å2 / Biso min: 48.38 Å2
Refinement stepCycle: final / Resolution: 2.85→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 70 88 2909
Biso mean--85.23 71.02 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.030.3791270.33122689281699
3.03-3.260.34951570.27992647280498
3.26-3.590.27531510.235626812832100
3.59-4.110.24061300.18727412871100
4.11-5.180.16061440.16232762290699
5.18-42.420.2031410.18932925306699
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)
18.55752.74013.74165.99642.72139.2073-0.0257-0.3476-0.95920.27440.20660.07210.5959-0.2186-0.02230.42580.0132-0.02450.5732-0.12180.6955-8.6743-29.669331.4982
23.25182.95861.35536.3587-1.26512.3984-0.01240.1929-0.0732-0.10940.18930.7045-0.1543-0.6448-0.15210.36960.1246-0.1080.7813-0.11580.6713-10.541-20.188731.2446
31.98020.5473-0.16742.70330.59592.92990.03570.16680.0169-0.0976-0.09190.1553-0.2943-0.19520.06060.41970.1237-0.08530.49-0.01810.39374.455-5.229934.4772
40.52821.6575-0.88735.4632-1.32059.75550.1331-0.2960.674-0.2760.47470.664-1.749-0.4246-0.45121.09540.1543-0.07710.6558-0.03870.8074.934615.749445.073
54.4567-0.538-1.0625.02081.67374.8140.02460.90630.1362-0.88810.0977-0.0177-0.77060.0056-0.06870.62240.0311-0.06140.69450.09420.45759.19470.699919.9968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 74 )A27 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 126 )A75 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 273 )A127 - 273
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 300 )A274 - 300
5X-RAY DIFFRACTION5chain 'A' and (resid 301 through 384 )A301 - 384

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