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- PDB-4nm3: Crystal structure of GSK-3/Axin complex bound to phosphorylated N... -

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Basic information

Entry
Database: PDB / ID: 4nm3
TitleCrystal structure of GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide
Components
  • Axin-1AXIN1
  • Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / phosphorylated N-terminal auto-inhibitory pS9 peptide / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


armadillo repeat domain binding / head development / cell development / regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / dorsal/ventral axis specification / negative regulation of type B pancreatic cell development ...armadillo repeat domain binding / head development / cell development / regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / dorsal/ventral axis specification / negative regulation of type B pancreatic cell development / axial mesoderm formation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / post-anal tail morphogenesis / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / tau-protein kinase / positive regulation of ubiquitin-dependent protein catabolic process / CRMPs in Sema3A signaling / heart valve development / 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 / Maturation of nucleoprotein / I-SMAD binding / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / nucleocytoplasmic transport / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of protein metabolic process / positive regulation of cell-matrix adhesion / regulation of axon extension / dopamine receptor signaling pathway / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / negative regulation of fat cell differentiation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / activation of protein kinase activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / NF-kappaB binding / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / canonical Wnt signaling pathway / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / signaling adaptor activity / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cytoplasmic microtubule organization / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / negative regulation of insulin receptor signaling pathway / positive regulation of protein export from nucleus / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / TCF dependent signaling in response to WNT / Ubiquitin-dependent degradation of Cyclin D / cell periphery / 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 / 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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / 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 / 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: 2.1 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.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

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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)48,03311
Polymers46,9992
Non-polymers1,0349
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-52 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.032, 81.032, 281.085
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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.) 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 / AXIN1 / 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, 206 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 277 K / Method: microdialysis / 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: 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: 2.1→38.963 Å / Num. all: 33107 / Num. obs: 33093 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 18.6 % / Biso Wilson estimate: 51.51 Å2 / Rsym value: 0.1 / Net I/σ(I): 24.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.1617.90.84692026284.88199.7
8085

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM7

4nm7


Resolution: 2.1→38.963 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.7731 / SU ML: 0.32 / σ(F): 1.9 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1658 5.04 %Transfer from related dataset
Rwork0.1943 ---
obs0.1966 32924 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.66 Å2 / Biso mean: 55.0237 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 62 197 3213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053174
X-RAY DIFFRACTIONf_angle_d0.914336
X-RAY DIFFRACTIONf_chiral_restr0.056497
X-RAY DIFFRACTIONf_plane_restr0.004550
X-RAY DIFFRACTIONf_dihedral_angle_d11.9431170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.16180.42811300.38752506263699
2.1618-2.23160.36151450.335525132658100
2.2316-2.31130.33431370.299525532690100
2.3113-2.40390.32271400.256525442684100
2.4039-2.51320.31911470.243125442691100
2.5132-2.64570.26451340.213525562690100
2.6457-2.81140.23651420.193125962738100
2.8114-3.02840.29361250.209425932718100
3.0284-3.3330.24071240.187526322756100
3.333-3.8150.21871340.170326472781100
3.815-4.80510.19521480.153326872835100
4.8051-38.96980.23041520.194428953047100
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)
13.1455-0.05570.84781.682-1.28851.2010.6824-0.5660.48490.37180.7012-1.15340.3197-0.0107-1.2521.31950.0829-0.2291.8097-0.28331.0189-20.855944.6289-23.0835
28.14481.956-0.66754.7919-0.50342.9013-0.1616-0.3950.97660.42830.05210.3824-0.485-0.1533-0.02860.4606-0.12570.10880.5990.00640.4285-14.815145.692.4732
31.0676-0.4019-1.75682.2788-0.26254.613-0.3040.2521-0.9045-0.0578-0.6581-1.0424-1.1054-0.29520.82010.8171-0.1699-0.15071.4555-0.02991.7308-24.559846.2167-16.6065
48.0359-1.9785-1.20575.2113.77724.9717-0.007-0.15190.2520.6143-0.2130.80860.4152-0.32630.19310.3249-0.14140.04310.39840.05410.3323-17.593639.706-3.8508
56.06670.9490.4873.69510.36063.8390.1528-0.1741-0.10250.2273-0.09210.06470.4392-0.1579-0.03570.36190.0162-0.05760.2806-0.02750.2448-5.529833.037-14.5813
62.4430.4348-0.64171.868-0.55024.87870.0401-0.1456-0.492-0.11150.02220.03780.82490.143-0.04240.47840.0277-0.10320.2641-0.0590.4114-3.473926.717-24.9527
73.64732.34-1.34645.6406-2.51584.7204-0.01790.61281.00630.03070.03620.0896-0.58530.2324-0.02150.5931-0.0805-0.07260.3391-0.01390.322-4.417943.2416-44.2805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 10 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 88 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 96 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 136 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 218 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 383 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 383 through 401 )B0

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