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- PDB-4nm7: Crystal structure of GSK-3/Axin complex bound to phosphorylated W... -

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Basic information

Entry
Database: PDB / ID: 4nm7
TitleCrystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif
Components
  • Axin-1
  • GSK3B protein
  • Phosphorylated Wnt receptor LRP6 e-motif
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / primed substrate / Kinase / Axin / phosphorylated Wnt receptor LRP6 e-motif / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


beta-catenin destruction complex assembly / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / neural crest formation / Signaling by RNF43 mutants / negative regulation of protein serine/threonine kinase activity / head development / cell development / kinase inhibitor activity ...beta-catenin destruction complex assembly / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / neural crest formation / Signaling by RNF43 mutants / negative regulation of protein serine/threonine kinase activity / head development / cell development / kinase inhibitor activity / toxin transmembrane transporter activity / 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 / Wnt receptor activity / axial mesoderm formation / superior temporal gyrus development / dorsal/ventral axis specification / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / low-density lipoprotein particle receptor activity / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / Wnt-protein binding / positive regulation of protein localization to centrosome / midbrain dopaminergic neuron differentiation / cellular response to cholesterol / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of protein kinase activity / positive regulation of cilium assembly / post-anal tail morphogenesis / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / dopaminergic neuron differentiation / regulation of microtubule-based process / regulation of protein export from nucleus / epigenetic programming in the zygotic pronuclei / frizzled binding / 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 / I-SMAD binding / cellular response to interleukin-3 / positive regulation of ubiquitin-dependent protein catabolic process / regulation of long-term synaptic potentiation / Wnt signalosome / 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 / neural crest cell differentiation / negative regulation of calcineurin-NFAT signaling cascade / nucleocytoplasmic transport / regulation of axon extension / Maturation of nucleoprotein / negative regulation of protein metabolic process / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / tau-protein kinase activity / 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 / regulation of neuron projection development / establishment of cell polarity / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of developmental process / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / dynactin binding / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / epithelial to mesenchymal transition / lateral plasma membrane / canonical Wnt signaling pathway / NF-kappaB binding / ubiquitin-like ligase-substrate adaptor activity / negative regulation of protein-containing complex assembly / negative regulation of signal transduction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
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 / Low density lipoprotein receptor-related protein 5/6 / : / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / Low density lipoprotein receptor-related protein 5/6 / : / 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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / 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 / Low-density lipoprotein receptor-related protein 6 / Glycogen synthase kinase-3 beta / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsStamos, J.L. / Chu, M.L.-H. / 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.3Oct 30, 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: GSK3B protein
B: Axin-1
C: Phosphorylated Wnt receptor LRP6 e-motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,54311
Polymers46,6013
Non-polymers9428
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-64 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.002, 82.002, 280.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GSK3B protein / GSK3beta isoform / Glycogen synthase kinase 3 beta / isoform CRA_b / cDNA FLJ75266 / highly similar ...GSK3beta isoform / Glycogen synthase kinase 3 beta / isoform CRA_b / cDNA FLJ75266 / highly similar to Homo sapiens glycogen synthase kinase 3 beta / mRNA


Mass: 42857.160 Da / Num. of mol.: 1 / Fragment: Residues 13-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B, hCG_1818062 / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL
References: UniProt: Q6FI27, UniProt: P49841*PLUS, tau-protein kinase

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Protein/peptide , 2 types, 2 molecules BC

#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
#3: Protein/peptide Phosphorylated Wnt receptor LRP6 e-motif


Mass: 1006.089 Da / Num. of mol.: 1 / Fragment: Residues 1603-1610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O75581*PLUS

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Non-polymers , 6 types, 114 molecules

#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2013
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.352 Å / Num. obs: 25932 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 60.05 Å2 / Rsym value: 0.136 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.2 % / Mean I/σ(I) obs: 0.9 / Rsym value: 4.307 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9U

1o9u


Resolution: 2.3→39.35 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.37 / σ(F): 1.91 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1292 5 %
Rwork0.183 --
obs0.185 25838 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 56 106 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043188
X-RAY DIFFRACTIONf_angle_d0.7594352
X-RAY DIFFRACTIONf_dihedral_angle_d12.2271178
X-RAY DIFFRACTIONf_chiral_restr0.05493
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.37531420.34512646X-RAY DIFFRACTION100
2.3921-2.5010.35171590.29062627X-RAY DIFFRACTION100
2.501-2.63280.34531350.25172673X-RAY DIFFRACTION100
2.6328-2.79770.30861430.22462658X-RAY DIFFRACTION100
2.7977-3.01370.27221450.22522704X-RAY DIFFRACTION100
3.0137-3.31680.26091170.19892727X-RAY DIFFRACTION100
3.3168-3.79640.24311380.17232740X-RAY DIFFRACTION100
3.7964-4.78180.19541550.13952787X-RAY DIFFRACTION100
4.7818-39.35780.1961580.17152984X-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)
16.74020.7198-0.84084.5902-1.30695.6228-0.3069-0.31470.90390.20630.17240.3564-0.38480.20980.13070.5595-0.17970.1250.7399-0.08050.5092-15.30247.11482.4315
26.3188-1.2069-1.35346.37954.08464.27570.10860.3220.29120.0272-0.24930.7911-0.0557-0.15640.13750.4036-0.16420.04180.62180.12820.5058-16.820241.784-4.3785
38.4084-0.06361.09843.6413-0.25774.43170.0754-0.3308-0.15870.0815-0.01180.02490.3573-0.2047-0.06150.4008-0.0142-0.0360.3525-0.01140.366-5.195333.2978-14.6389
42.80710.6182-0.31992.2144-1.10956.32160.0242-0.0916-0.6369-0.26140.05930.04960.91810.0183-0.06220.58960.0076-0.10090.2981-0.04920.5717-3.301627.0388-24.9587
53.0962-0.27370.62586.2782-3.19739.47720.49611.11620.9579-0.6858-0.15190.1708-0.32490.1201-0.26980.9541-0.1079-0.07580.39750.01560.5389-4.578343.4152-44.2255
69.6818.17235.43139.7733.68793.32680.8079-0.96780.34120.406-0.2715-1.3412-0.6271-1.052-0.39930.9250.1694-0.24841.2714-0.06561.3107-20.925344.7492-22.6669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 25:74 )A25 - 74
2X-RAY DIFFRACTION2( CHAIN A AND RESID 75:138 )A75 - 138
3X-RAY DIFFRACTION3( CHAIN A AND RESID 139:218 )A139 - 218
4X-RAY DIFFRACTION4( CHAIN A AND RESID 219:384 )A219 - 384
5X-RAY DIFFRACTION5( CHAIN B AND RESID 383:401 )B383 - 401
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1604:1609 )C1604 - 1609

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