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- PDB-4nu1: Crystal structure of a transition state mimic of the GSK-3/Axin c... -

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Basic information

Entry
Database: PDB / ID: 4nu1
TitleCrystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide
Components
  • Axin-1
  • Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / GSK-3 / Axin / kinase / primed substrate / transition state / phosphorylated N-terminal auto-inhibitory pS9 peptide / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / Disassembly of the destruction complex and recruitment of AXIN to the membrane ...hepatic stellate cell activation / B-WICH complex positively regulates rRNA expression / negative regulation of synaptic assembly at neuromuscular junction / Regulation of HSF1-mediated heat shock response / negative regulation of protein localization to centrosome / re-entry into mitotic cell cycle / negative regulation of neuron maturation / Beta-catenin phosphorylation cascade / CRMPs in Sema3A signaling / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of synaptic assembly at neuromuscular junction / membrane-bounded organelle / positive regulation of osteoclast proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / armadillo repeat domain binding / myotube differentiation / negative regulation of neuron migration / positive regulation of cardiac muscle cell differentiation / cell growth involved in cardiac muscle cell development / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / head development / negative regulation of dendrite morphogenesis / Degradation of beta-catenin by the destruction complex / cell development / protein localization to microtubule / neuron projection organization / positive regulation of stem cell differentiation / negative regulation of cardiac muscle hypertrophy / dorsal/ventral axis specification / axial mesoderm formation / negative regulation of dendrite development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / GLI3 is processed to GLI3R by the proteasome / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / autosome genomic imprinting / meiosis I / positive regulation of cilium assembly / negative regulation of protein acetylation / post-anal tail morphogenesis / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / bone remodeling / beta-catenin destruction complex / tau-protein kinase / positive regulation of ubiquitin-dependent protein catabolic process / myoblast fusion / epigenetic programming in the zygotic pronuclei / regulation of microtubule-based process / regulation of modification of postsynaptic structure / 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 osteoclast differentiation / I-SMAD binding / axon extension / cellular response to interleukin-3 / negative regulation of TOR signaling / Wnt signalosome / meiotic spindle / 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 / negative regulation of protein metabolic process / positive regulation of mitochondrial membrane potential / nucleocytoplasmic transport / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cellular response to glucocorticoid stimulus / negative regulation of epithelial to mesenchymal transition / negative regulation of calcineurin-NFAT signaling cascade / regulation of osteoblast differentiation / regulation of axon extension / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / regulation of axonogenesis / regulation of dendrite morphogenesis / tau-protein kinase activity / establishment of cell polarity / establishment or maintenance of cell polarity / activation of protein kinase activity / RUNX1 regulates transcription of genes involved in WNT signaling / response to zinc ion / RUNX1 regulates estrogen receptor mediated transcription / glycogen metabolic process / ER overload response / dynein complex binding / negative regulation of fat cell differentiation / hepatocyte apoptotic process / regulation of neuron projection development / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of osteoblast proliferation / negative regulation of transcription elongation by RNA polymerase II
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 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / NITRATE ION / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,8059
Polymers46,9992
Non-polymers8067
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-43 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.997, 80.997, 280.530
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: 44260.605 Da / Num. of mol.: 1 / Fragment: Residues 1-383 with phosphoylated Ser9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsk3b / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-plus RIL
References: UniProt: Q9WV60, 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: AXIN1, AXIN / 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, 105 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / 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-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#7: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 10% PEG 35,000, 20mM Tris pH7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2013 / Details: mirrors
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→46.76 Å / Num. all: 19925 / Num. obs: 19922 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 21 % / Biso Wilson estimate: 60.85 Å2 / Rsym value: 0.303 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 21.6 % / Mean I/σ(I) obs: 0.7 / Rsym value: 6.772 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.8data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM3

4nm3


Resolution: 2.5→40.498 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 974 4.91 %
Rwork0.1913 --
obs0.1939 19823 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.7733 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 49 98 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033134
X-RAY DIFFRACTIONf_angle_d0.6334283
X-RAY DIFFRACTIONf_dihedral_angle_d9.6011143
X-RAY DIFFRACTIONf_chiral_restr0.026488
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.34981360.32782603X-RAY DIFFRACTION100
2.6318-2.79660.32681420.28952614X-RAY DIFFRACTION100
2.7966-3.01250.35031330.26532638X-RAY DIFFRACTION100
3.0125-3.31550.30891200.23132659X-RAY DIFFRACTION100
3.3155-3.7950.21891390.18042683X-RAY DIFFRACTION100
3.795-4.78010.22161490.14422724X-RAY DIFFRACTION100
4.7801-40.50380.2151550.1742928X-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)
14.070.2075-3.54852.0188-0.71143.53330.0185-1.43712.41611.76721.6975-2.42430.23671.4055-2.0831.5215-0.2207-0.14411.8291-0.40341.5381-21.834845.0296-22.8722
27.2342.4148-0.85598.0168-1.30713.739-0.0055-0.80730.84970.4515-0.16730.1715-0.4479-0.19260.17780.5085-0.12230.12190.6948-0.0090.601-14.975345.53062.0608
36.7607-2.7828-2.42096.9667-2.88143.4499-0.22770.18840.33870.5716-0.7869-2.0778-1.0605-0.27960.94711.1336-0.0757-0.1691.5887-0.13661.4187-25.200446.475-15.7124
46.6714-1.1806-3.46018.02894.82126.08720.37030.30480.19610.412-0.5690.8870.3216-0.6830.18370.4915-0.12410.05370.69640.10360.5091-17.889839.9169-3.846
53.30281.31630.25985.16990.13895.04110.0274-0.0699-0.19490.1277-0.0291-0.00890.4932-0.30610.01220.5027-0.002-0.04680.4599-0.02390.45-5.655233.138-14.4699
63.12120.6346-0.93542.4542-1.03835.79930.02290.0029-0.5247-0.25370.01850.02850.9850.0834-0.06560.60020.0109-0.10580.3717-0.09210.5421-3.722726.7658-24.9203
72.1954-0.0803-2.53892.51-3.39418.29790.1950.98150.4549-0.3637-0.2142-0.0483-0.72160.0268-0.05010.8596-0.1185-0.10280.53450.02060.6552-4.244643.2426-44.1084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 383 )
7X-RAY DIFFRACTION7chain 'B' and (resid 383 through 401 )

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