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- PDB-1o9u: GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH AXIN PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1o9u
TitleGLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH AXIN PEPTIDE
Components
  • AXIN PEPTIDE
  • GLYCOGEN SYNTHASE KINASE-3 BETA
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX / KINASE / INSULIN PATHWAY / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / MULTIGENE FAMILY / PHOSPHORYLATION / DEVELOPMENTAL PROTEIN / ANTI-ONCOGENE / APOPTOSIS / TRANSFERASE- TRANSFERASE SUBSTRATE COMPLEX
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 / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / tau-protein kinase / 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 / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / I-SMAD binding / epigenetic programming in the zygotic pronuclei / Maturation of nucleoprotein / cellular response to interleukin-3 / positive regulation of ubiquitin-dependent protein catabolic 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 / nucleocytoplasmic transport / negative regulation of protein metabolic process / regulation of axon extension / 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 / ER overload response / glycogen metabolic process / negative regulation of fat cell differentiation / establishment of cell polarity / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of neuron projection development / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / R-SMAD binding / dynactin binding / negative regulation of transcription elongation by RNA polymerase II / lateral plasma membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / NF-kappaB binding / 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 / positive regulation of protein ubiquitination / signaling adaptor activity / cytoplasmic microtubule organization / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / TCF dependent signaling in response to WNT / Transcriptional and post-translational regulation of MITF-M expression and activity / Ubiquitin-dependent degradation of Cyclin D / regulation of microtubule cytoskeleton organization / protein serine/threonine kinase binding / response to endoplasmic reticulum stress / negative regulation of cell migration / protein serine/threonine kinase activator activity / Degradation of AXIN
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
9-METHYL-9H-PURIN-6-AMINE / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDajani, R. / Pearl, L.H. / Roe, S.M.
CitationJournal: Embo J. / Year: 2003
Title: Structural Basis for Recruitment of Glycogen Synthase Kinase 3Beta to the Axin-Apc Scaffold Complex
Authors: Dajani, R. / Fraser, E. / Roe, S.M. / Yeo, M. / Good, V. / Thompson, V. / Dale, T.C. / Pearl, L.H.
History
DepositionDec 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9113
Polymers41,7622
Non-polymers1491
Water2,396133
1
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: AXIN PEPTIDE
hetero molecules

A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: AXIN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8226
Polymers83,5244
Non-polymers2982
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
MethodPQS
Unit cell
Length a, b, c (Å)81.950, 81.950, 282.440
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 / GSK3B


Mass: 39622.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-384
Source method: isolated from a genetically manipulated source
Details: PHOSPHOTYROSINE AT A216 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC HTA / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P49841, EC: 2.7.1.37
#2: Protein/peptide AXIN PEPTIDE / AXIS INHIBITION PROTEIN 1 / HAXIN / AXIN1 / AXIN


Mass: 2139.428 Da / Num. of mol.: 1 / Fragment: RESIDUES 383-400 / Source method: obtained synthetically / Details: AXIN PEPTIDE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O15169
#3: Chemical ChemComp-ADZ / 9-METHYL-9H-PURIN-6-AMINE


Mass: 149.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL ...Details: CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL PRECIPITANT (18% PEG4000, 150MM MGCL2, 100MM TRIS- HCL, PH 7.5)
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlGSK3beta1drop
20.37 mg/mlaxin1drop
325 mMHEPES-NaOH1droppH7.0
4250 mM1dropNaCl
51 mMdithiothreitol1drop
618 %PEG40001reservoir
7150 mM1reservoirMgCl2
8100 mMTris-HCl1reservoirpH7.5
91
101
111
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9253
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 2.4→24 Å / Num. obs: 22740 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.076 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.305 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 99.7 % / Redundancy: 3.9 % / Num. unique obs: 3252 / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8F

1h8f


Resolution: 2.4→23.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2031993.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1132 5 %RANDOM
Rwork0.233 ---
obs0.233 22658 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.15 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.08 Å25.26 Å20 Å2
2--4.08 Å20 Å2
3----8.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→23.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 11 133 3086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 189 5.1 %
Rwork0.276 3523 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ADE_GOL.PARADE_GOL.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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