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- PDB-4b7t: Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and L... -

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Basic information

Entry
Database: PDB / ID: 4b7t
TitleGlycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Leucettine L4
Components
  • AXIN-1
  • GLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / TRANSFERASE / INSULIN PATHWAY / WNT SIGNALING PATHWAY / INHIBITOR
Function / homology
Function and homology information


beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / axial mesoderm formation ...beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / axial mesoderm formation / dorsal/ventral axis specification / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / post-anal tail morphogenesis / beta-catenin destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-3 / Maturation of nucleoprotein / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei / regulation of microtubule-based process / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / negative regulation of protein metabolic process / nucleocytoplasmic transport / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / glycogen metabolic process / ER overload response / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / establishment of cell polarity / protein kinase A catalytic subunit binding / R-SMAD binding / dynactin binding / negative regulation of transcription elongation by RNA polymerase II / epithelial to mesenchymal transition / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / NF-kappaB binding / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / positive regulation of protein binding / negative regulation of protein-containing complex assembly / ubiquitin-like ligase-substrate adaptor activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / cytoplasmic microtubule organization / signaling adaptor activity / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / Transcriptional and post-translational regulation of MITF-M expression and activity / presynaptic modulation of chemical synaptic transmission / protein serine/threonine kinase binding / regulation of microtubule cytoskeleton organization / negative regulation of cell migration / response to endoplasmic reticulum stress / positive regulation of protein export from nucleus / protein serine/threonine kinase activator activity / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Glycogen synthase kinase 3, catalytic domain / : / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Ubiquitin-like domain superfamily / 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
Chem-CWT / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.772 Å
AuthorsOberholzer, A.E. / Pearl, L.H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Selectivity, Cocrystal Structures, and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.
Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A.E. / Pearl, L.H. / Carreaux, F. / Bazureau, J. / Knapp, S. / Meijer, L.
History
DepositionAug 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2303
Polymers41,9422
Non-polymers2871
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13.6 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.577, 81.577, 283.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / GSK-3 BETA / SERINE/THREONINE-PROTEIN KINASE GSK3B


Mass: 39802.793 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide AXIN-1 / AXIS INHIBITION PROTEIN 1 / HAXIN


Mass: 2139.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 383-400 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O15169
#3: Chemical ChemComp-CWT / (5Z)-5-(1,3-benzodioxol-5-ylmethylidene)-3-methyl-2-(propan-2-ylamino)imidazol-4-one / Leucettine L4


Mass: 287.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.12 Å3/Da / Density % sol: 60.57 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL, PH 8.0, 0.15 M MGCL2, 15% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.77→29.99 Å / Num. obs: 14709 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 46.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellResolution: 2.77→2.94 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.1 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9U

1o9u


Resolution: 2.772→29.986 Å / SU ML: 0.36 / σ(F): 1.38 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 747 5.1 %
Rwork0.1952 --
obs0.1973 14707 97.66 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.653 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6648 Å20 Å20 Å2
2--5.6648 Å20 Å2
3----11.3297 Å2
Refinement stepCycle: LAST / Resolution: 2.772→29.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 21 53 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023042
X-RAY DIFFRACTIONf_angle_d0.5854139
X-RAY DIFFRACTIONf_dihedral_angle_d12.291147
X-RAY DIFFRACTIONf_chiral_restr0.039461
X-RAY DIFFRACTIONf_plane_restr0.003533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7722-2.9860.31111460.26262572X-RAY DIFFRACTION93
2.986-3.28620.28651460.23682764X-RAY DIFFRACTION99
3.2862-3.76090.24061470.20422794X-RAY DIFFRACTION99
3.7609-4.73540.20051480.16542822X-RAY DIFFRACTION98
4.7354-29.98790.21621600.17893008X-RAY DIFFRACTION98
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)
10.01540.0193-0.01120.0182-0.0020.0163-0.0115-0.07820.02660.0892-0.03950.09580.0086-0.0377-0.03160.1771-0.14570.24040.43410.01340.179-16.348245.04453.2618
20.02480.0080.02920.00180.00710.0508-0.03630.003-0.00740.0043-0.0580.00090.0146-0.024-0.00580.1532-0.04890.08230.31740.01080.2583-21.921142.1742-5.7381
30.0071-0.0081-0.02420.01480.00210.04310.0662-0.0625-0.02430.04760.0647-0.04190.0727-0.05540.1150.0879-0.0412-0.04930.1460.01750.1208-4.291234.3249-10.944
40.0047-0.0005-0.00290.0023-0.00110.0021-0.0007-0.0168-0.01410.0045-0.00330.0233-0.00710.0309-00.2465-0.0096-0.00430.42970.08030.3568-20.245337.4637-22.4653
5-0.0013-0.00080.0002-0.00390.00110.0033-0.0038-0.0374-0.0191-0.03550.02670.05180.0201-0.0051-0.00570.0152-0.071-0.1775-0.0149-0.0739-0.1687-4.814836.84-28.7195
60.0359-0.005-0.03440.00520.0070.0257-0.01340.0644-0.1418-0.1077-0.05260.01970.0874-0.0346-0.10390.2952-0.0505-0.19620.0412-0.0897-0.0275-2.983426.6109-31.7146
70.0303-0.01290.01040.0099-0.00230.0297-0.0339-0.0538-0.03340.0529-0.0287-0.03290.03360.04650.00650.3623-0.1241-0.17660.2310.18170.4839-5.652315.8579-7.9307
80.0070.00430.00560.00390.0030.00760.01770.0240.0093-0.02030.02190.02210.0063-0.00960.00390.2576-0.0285-0.04940.07010.05320.2699-5.742444.4938-44.527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 35:89)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 90:125)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 126:198)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 199:218)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 219:273)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 274:344)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 345:384)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 383:400)

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