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- PDB-3pup: Structure of Glycogen Synthase Kinase 3 beta (GSK3B) in complex w... -

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Basic information

Entry
Database: PDB / ID: 3pup
TitleStructure of Glycogen Synthase Kinase 3 beta (GSK3B) in complex with a ruthenium octasporine ligand (OS1)
ComponentsGlycogen synthase kinase-3 beta
KeywordsTRANSFERASE / WNT SIGNALING PATHWAY / SERINE/THREONINE-PROTEIN KINASE / RUTHENIUM GLYCOGEN SYNTHASE KINASE PICOMOLAR / NUCLEOTIDE-BINDING / KINASE / ATP-BINDING / PHOSPHOPROTEIN
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 / regulation of axon extension / Wnt signalosome / 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 / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / regulation of cellular response to heat / cellular response to retinoic acid / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / 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 / neuron projection development / cellular response to amyloid-beta / positive regulation of protein catabolic process / 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
Ruthenium octasporine / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 Å
AuthorsFilippakopoulos, P. / Kraling, K. / Essen, L.O. / Meggers, E. / Knapp, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2011
Title: Structurally sophisticated octahedral metal complexes as highly selective protein kinase inhibitors.
Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. ...Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. / Knapp, S. / Essen, L.O. / Meggers, E.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Targeting large kinase active site with rigid, bulky octahedral ruthenium complexes.
Authors: Maksimoska, J. / Feng, L. / Harms, K. / Yi, C. / Kissil, J. / Marmorstein, R. / Meggers, E.
#2: Journal: Chembiochem / Year: 2008
Title: Extremely tight binding of a ruthenium complex to glycogen synthase kinase 3.
Authors: Atilla-Gokcumen, G.E. / Pagano, N. / Streu, C. / Maksimoska, J. / Filippakopoulos, P. / Knapp, S. / Meggers, E.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7484
Polymers93,6022
Non-polymers1,1462
Water0
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3742
Polymers46,8011
Non-polymers5731
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3742
Polymers46,8011
Non-polymers5731
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-11 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.320, 84.300, 178.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA35 - 9035 - 90
21SERSERASPASPBB35 - 9035 - 90
12LYSLYSARGARGAA91 - 14491 - 144
22LYSLYSARGARGBB91 - 14491 - 144
13HISHISARGARGAA145 - 282145 - 282
23HISHISARGARGBB145 - 282145 - 282
14GLUGLUALAALAAA283 - 382283 - 382
24GLUGLUALAALABB283 - 382283 - 382
DetailsMonomer

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Components

#1: Protein Glycogen synthase kinase-3 beta / / GSK-3 beta


Mass: 46801.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P49841, tau-protein kinase
#2: Chemical ChemComp-OS1 / Ruthenium octasporine


Mass: 572.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H16ClN6O3Ru

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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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM Tris pH 7.4 20 % PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Av σ(I) over netI: 3.8 / Number: 126289 / Rsym value: 0.186 / D res high: 2.99 Å / D res low: 48.542 Å / Num. obs: 25273 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.4648.5494.310.0610.0614.6
6.699.4695.510.0840.0844.9
5.466.6996.410.1410.1415
4.735.4696.810.1390.1395
4.234.739710.1350.1355
3.864.2397.410.1730.1735
3.573.8697.610.2390.2395.1
3.343.5798.310.3440.3445
3.153.3497.710.5430.5435
2.993.1597.710.7720.7724.9
ReflectionResolution: 2.99→49.33 Å / Num. all: 25974 / Num. obs: 25273 / % possible obs: 97.3 % / Redundancy: 5 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.186 / Rsym value: 0.186 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.99-3.154.90.77211806836510.77297.7
3.15-3.3450.5431.41752334740.54397.7
3.34-3.5750.3442.21641432660.34498.3
3.57-3.865.10.2393.11538030410.23997.6
3.86-4.2350.1734.11413028040.17397.4
4.23-4.7350.1355.21266425260.13597
4.73-5.4650.1394.91121222360.13996.8
5.46-6.6950.1414.9957219130.14196.4
6.69-9.464.90.0847.8739615010.08495.5
9.46-48.5424.60.0619.539308610.06194.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.99 Å48.54 Å
Translation2.99 Å48.54 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLD

2jld


Resolution: 2.99→49.33 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.2424 / WRfactor Rwork: 0.1949 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8603 / SU B: 32.968 / SU ML: 0.279 / SU R Cruickshank DPI: 0.9485 / SU Rfree: 0.3634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1274 5.1 %RANDOM
Rwork0.2042 ---
all0.2064 26104 --
obs0.2064 25227 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 125.04 Å2 / Biso mean: 51.9741 Å2 / Biso min: 5.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--4.89 Å20 Å2
3----5.5 Å2
Refinement stepCycle: LAST / Resolution: 2.99→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 70 0 5394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225540
X-RAY DIFFRACTIONr_bond_other_d0.0020.023616
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9947563
X-RAY DIFFRACTIONr_angle_other_deg0.97138850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38723.607219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30715833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216107
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021081
X-RAY DIFFRACTIONr_mcbond_it2.45233481
X-RAY DIFFRACTIONr_mcbond_other1.19231362
X-RAY DIFFRACTIONr_mcangle_it4.1855640
X-RAY DIFFRACTIONr_scbond_it6.81382059
X-RAY DIFFRACTIONr_scangle_it9.525111923
X-RAY DIFFRACTIONr_sphericity_bonded16.1832
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4441 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.040.05
TIGHT THERMAL0.120.5
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 96 -
Rwork0.304 1737 -
all-1833 -
obs--96.68 %
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)
14.4498-2.5521-1.47053.56430.50621.99370.13590.3036-0.4841-0.2526-0.09530.10580.13870.2367-0.04060.0493-0.0024-0.05240.242-0.00960.154528.8899-21.3888-7.7687
21.6251-0.03480.19081.6019-1.04742.68010.06160.00060.1590.0788-0.02430.0637-0.4028-0.0804-0.03730.0976-0.00510.0020.1406-0.03510.037116.26811.2507-1.9279
33.6741-2.7338-0.87024.21881.06652.41340.0626-0.04240.02120.2385-0.00170.445-0.4048-0.54-0.0610.24850.04230.0140.17750.0730.1572-0.481415.7743-35.4994
41.71240.2086-0.00081.9132-0.17274.0543-0.03450.0783-0.1674-0.05030.0267-0.11030.18480.33180.00780.078-0.04940.01760.12530.00670.041721.45641.2754-39.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 144
2X-RAY DIFFRACTION2A145 - 382
3X-RAY DIFFRACTION3B35 - 144
4X-RAY DIFFRACTION4B145 - 383

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