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- PDB-4nm0: Crystal structure of peptide inhibitor-free GSK-3/Axin complex -

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Basic information

Entry
Database: PDB / ID: 4nm0
TitleCrystal structure of peptide inhibitor-free GSK-3/Axin complex
Components
  • Axin-1
  • Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / TRANSFERASE-PEPTIDE 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 / superior temporal gyrus development / dorsal/ventral axis specification / 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 / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / epigenetic programming in the zygotic pronuclei / Maturation of nucleoprotein / I-SMAD binding / 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 / regulation of axon extension / negative regulation of protein metabolic process / Maturation of nucleoprotein / tau-protein kinase activity / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / 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 / regulation of neuron projection development / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / dynactin binding / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / NF-kappaB binding / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / negative regulation of protein-containing complex assembly / 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 / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / cytoplasmic microtubule organization / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / protein serine/threonine kinase binding / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / protein serine/threonine kinase activator activity / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / cell periphery / excitatory postsynaptic potential / hippocampus development
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
ADENOSINE-5'-DIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChu, M.L.-H. / Stamos, J.L. / Enos, M.D. / Shah, N. / Weis, W.I.
CitationJournal: Elife / Year: 2014
Title: Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.
Authors: Stamos, J.L. / Chu, M.L. / Enos, M.D. / Shah, N. / Weis, W.I.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,04512
Polymers46,9192
Non-polymers1,12610
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-56 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.303, 81.303, 280.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 44180.625 Da / Num. of mol.: 1 / Fragment: Residues 1-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 2738.144 Da / Num. of mol.: 1 / Fragment: Residues 383-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN, AXIN1 / Plasmid: Modified pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O15169

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Non-polymers , 6 types, 174 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.83 Å3/Da / Density % sol: 56.5 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 20mM MgCl2, 400uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→39.05 Å / Num. obs: 20069 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Rrim(I) all: 0.112 / Rsym value: 0.106 / Net I/σ(I): 18.4 / Num. measured all: 192347
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.5-2.69.91.22177022060.7260.5761.8391.74399.9
396910.0060.017

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM7

4nm7


Resolution: 2.5→39.048 Å / SU ML: 0.34 / σ(F): 1.91 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 979 4.91 %Transfer from related dataset
Rwork0.1908 ---
obs0.1931 19958 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 68 164 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033079
X-RAY DIFFRACTIONf_angle_d0.6264198
X-RAY DIFFRACTIONf_dihedral_angle_d11.8611128
X-RAY DIFFRACTIONf_chiral_restr0.041479
X-RAY DIFFRACTIONf_plane_restr0.003536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.32491380.31632621X-RAY DIFFRACTION100
2.6318-2.79670.28711390.26172638X-RAY DIFFRACTION100
2.7967-3.01250.29651380.23372650X-RAY DIFFRACTION100
3.0125-3.31560.30461170.21142681X-RAY DIFFRACTION100
3.3156-3.7950.24711390.17872696X-RAY DIFFRACTION100
3.795-4.77990.20191530.15422752X-RAY DIFFRACTION100
4.7799-39.05270.22241550.18362941X-RAY DIFFRACTION100
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)
15.49370.748-0.24182.0887-1.70323.3373-0.118-0.48310.62140.583-0.02840.3761-0.784-0.0901-0.69550.5247-0.10220.16890.5912-0.06730.482-16.195545.74723.2834
22.19150.4531-0.56592.63961.47321.73520.17720.4220.16230.1901-0.30180.66540.3517-0.56240.03850.409-0.05220.0580.58230.03540.4175-19.443741.3012-4.8623
32.8757-0.2407-0.69522.3589-0.1692.25720.1949-0.18520.02050.2539-0.1097-0.12380.3694-0.2114-0.01340.4153-0.0349-0.05730.3319-0.0090.2876-5.73933.209-14.342
41.86710.34660.09061.1119-0.61373.78430.02380.0276-0.3168-0.12850.0498-0.03210.52610.0699-0.00050.41480.0044-0.07250.2774-0.07190.3561-3.895726.9964-24.9416
54.40111.07380.76093.3652-0.66733.7710.09480.53680.8424-0.53320.0070.2285-0.7624-0.2608-0.0320.672-0.1132-0.02260.44760.00170.3617-5.500843.8954-43.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 383 )
5X-RAY DIFFRACTION5chain 'B' and (resid 381 through 401 )

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