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- PDB-7sxj: BIO-2895 (BRD0705) bound GSK3beta-axin complex -

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Basic information

Entry
Database: PDB / ID: 7sxj
TitleBIO-2895 (BRD0705) bound GSK3beta-axin complex
Components
  • Glycogen synthase kinase-3 beta
  • axin peptide
KeywordsHYDROLASE / kinase
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 / superior temporal gyrus development / 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 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 / superior temporal gyrus development / 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 / CRMPs in Sema3A signaling / tau-protein kinase / heart valve development / 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 / regulation of protein export from nucleus / cellular response to interleukin-3 / 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 / regulation of long-term synaptic potentiation / Wnt signalosome / negative regulation of TOR signaling / regulation of microtubule-based process / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of protein binding / regulation of axon extension / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / negative regulation of protein localization to nucleus / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / positive regulation of cell-matrix adhesion / glycogen metabolic process / ER overload response / regulation of axonogenesis / regulation of dendrite morphogenesis / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / establishment of cell polarity / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / NF-kappaB binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein-containing complex assembly / 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 type I interferon production / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of autophagy / response to endoplasmic reticulum stress / negative regulation of cell migration / positive regulation of protein export from nucleus / presynaptic modulation of chemical synaptic transmission / positive regulation of protein ubiquitination / peptidyl-serine phosphorylation / regulation of microtubule cytoskeleton organization / hippocampus development / positive regulation of cell differentiation / mitochondrion organization / Ubiquitin-dependent degradation of Cyclin D / positive regulation of protein-containing complex assembly / excitatory postsynaptic potential / negative regulation of canonical Wnt signaling pathway / circadian rhythm / regulation of circadian rhythm / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / B-WICH complex positively regulates rRNA expression / beta-catenin binding / Degradation of beta-catenin by the destruction complex / tau protein binding / cellular response to amyloid-beta / Wnt signaling pathway / neuron projection development / kinase activity / p53 binding / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / insulin receptor signaling pathway / protein autophosphorylation
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-6VL / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChodaparambil, J.V.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Chem Neurosci / Year: 2023
Title: Elucidation of the GSK3 alpha Structure Informs the Design of Novel, Paralog-Selective Inhibitors.
Authors: Amaral, B. / Capacci, A. / Anderson, T. / Tezer, C. / Bajrami, B. / Lulla, M. / Lucas, B. / Chodaparambil, J.V. / Marcotte, D. / Kumar, P.R. / Murugan, P. / Spilker, K. / Cullivan, M. / ...Authors: Amaral, B. / Capacci, A. / Anderson, T. / Tezer, C. / Bajrami, B. / Lulla, M. / Lucas, B. / Chodaparambil, J.V. / Marcotte, D. / Kumar, P.R. / Murugan, P. / Spilker, K. / Cullivan, M. / Wang, T. / Peterson, A.C. / Enyedy, I. / Ma, B. / Chen, T. / Yousaf, Z. / Calhoun, M. / Golonzhka, O. / Dillon, G.M. / Koirala, S.
History
DepositionNov 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: axin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2453
Polymers41,9242
Non-polymers3211
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-16 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.090, 73.870, 82.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 39883.719 Da / Num. of mol.: 1
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: Protein/peptide axin peptide


Mass: 2040.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-6VL / (4~{S})-4-ethyl-7,7-dimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one


Mass: 321.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate, 0.1M BisTRIS pH 7.0, 5% Glycerol and 17% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→36.94 Å / Num. obs: 36269 / % possible obs: 99.93 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.78 Å2 / CC1/2: 0.99 / Net I/σ(I): 29.13
Reflection shellResolution: 1.85→1.91 Å / Num. unique obs: 3551 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kpl

5kpl


Resolution: 1.85→36.94 Å / SU ML: 0.2347 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2034 1999 5.51 %
Rwork0.1838 34270 -
obs0.1849 36269 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.94 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 24 213 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422946
X-RAY DIFFRACTIONf_angle_d0.74684033
X-RAY DIFFRACTIONf_chiral_restr0.0482460
X-RAY DIFFRACTIONf_plane_restr0.0105520
X-RAY DIFFRACTIONf_dihedral_angle_d6.0161430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.37311320.32932284X-RAY DIFFRACTION94.82
1.89-1.940.27381350.26422442X-RAY DIFFRACTION100
1.94-20.29461520.22652395X-RAY DIFFRACTION99.96
2-2.060.25481320.22412451X-RAY DIFFRACTION100
2.06-2.140.25821490.22552410X-RAY DIFFRACTION100
2.14-2.220.29161350.20882432X-RAY DIFFRACTION100
2.22-2.330.26531420.20512429X-RAY DIFFRACTION99.88
2.33-2.450.25951450.19022444X-RAY DIFFRACTION100
2.45-2.60.2161430.19732450X-RAY DIFFRACTION100
2.6-2.80.22211440.19942439X-RAY DIFFRACTION100
2.8-3.080.23231440.1992486X-RAY DIFFRACTION99.96
3.08-3.530.19091420.18542478X-RAY DIFFRACTION100
3.53-4.450.15181490.15092508X-RAY DIFFRACTION99.96
4.45-36.940.17531550.16332622X-RAY DIFFRACTION99.61
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)
19.61809740581.20259169255-3.197186708147.494978995280.7144638790226.88178023170.2025127303580.1869968671290.0503127238258-0.501333881753-0.0369036213913-0.2587631142710.1421675164720.371009821869-0.2438479008770.259777744694-0.03245395528670.08098955265610.383990149946-0.07140036943530.26936483505825.3928231146-5.5376293381417.7517099038
27.439565810051.43315919172-2.14342882775.84901587948-0.9705714116797.30716761778-0.10900449997-0.233574151066-0.591235881030.2195695583740.222692720073-0.1672809642230.4458820376530.3092054486030.01084630341250.306926721840.109979928872-0.02195824403160.4581081104350.05976458691780.38570901615922.6195008172-11.888186144826.1110633037
34.677940390720.0103912967641.771007381683.980145578070.4174672372017.805122782590.0076829117053-0.0709034534266-0.0512362225167-0.1837159373980.144463780569-0.1430954898340.07097619059390.129351225485-0.1408556062140.247332736523-0.01290547688710.07130913654930.234253755902-0.02770393598540.22977339078414.6180793188-7.6439607036518.4993685057
43.425782718-2.03594462977-3.336008925842.17534276582.063911168886.70673604874-0.311833942538-0.344238258863-0.2690209292570.2401613717050.20303296009-0.08660109650460.6489988215190.4523241916320.1466549314110.2576932972370.00288355447603-0.04162586044890.3023807393420.001294601424980.33586957919812.5326517576-6.328425813130.7812445084
53.36168632928-0.1693663961550.1018498757133.252596188650.1743428945866.357056542880.04361648793590.300935540733-0.264121520534-0.0937633533868-0.007589868230410.02459778891820.298881732216-0.190969231507-0.07777385468640.2204821447540.00632948559951-0.001695544362980.230075028789-0.009785715578770.3008762670431.65180440377-0.55787202381729.2645631954
65.798364049460.6327303774111.118691672442.188906066460.1487820533263.337543559110.1570047624170.057480717065-0.608326578013-0.0680378305584-0.00244803062590.3070109633240.485213353072-0.810971386828-0.134631106220.297316427572-0.0621098032267-0.02730004342170.365645743930.007921677402960.396762532523-15.1848568196-6.7698118802633.645232587
74.195777999851.29354900421-0.02488767253932.351652505320.1863787700013.126525275060.0992836534372-0.0708088592250.307449550290.170207087348-0.004144580438930.212776348063-0.30552891969-0.376603358892-0.0687798977650.3111244346970.08067475741230.01761490283160.2827244182630.008891417933570.293860416095-8.682672791227.5942832132638.3607527198
84.43561607741-1.190745978013.123722752762.30925670882-3.297924451878.59315375583-0.125243535740.1584587469080.6705390938930.362829986016-0.230083813414-0.244813341499-0.8886950212210.6982806754750.3460906804090.473311317447-0.0695844601132-0.01090430140450.29201693128-0.01862499304860.4251443582795.4497420295816.938700694934.7951602278
92.35354899787-0.1688361288880.7495095839639.35982500715.442025019093.473483063680.259820266923-0.264500081783-1.281676553770.6966084564-1.065253005860.4779428828141.87853951599-1.345205343590.8697197942330.64071987674-0.225325415443-0.05472481632990.853735482460.002437866864711.12073996063-23.4663874833-18.104508445431.3720722687
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 51 )AA33 - 511 - 19
22chain 'A' and (resid 52 through 74 )AA52 - 7420 - 39
33chain 'A' and (resid 75 through 103 )AA75 - 10340 - 68
44chain 'A' and (resid 104 through 154 )AA104 - 15469 - 118
55chain 'A' and (resid 155 through 219 )AA155 - 219119 - 183
66chain 'A' and (resid 220 through 304 )AA220 - 304184 - 268
77chain 'A' and (resid 305 through 344 )AA305 - 344269 - 308
88chain 'A' and (resid 345 through 383 )AA345 - 383309 - 347
99chain 'B' and (resid 384 through 400 )BB384 - 4001 - 17

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