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- PDB-4nm5: Crystal structure of GSK-3/Axin complex bound to phosphorylated W... -

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Basic information

Entry
Database: PDB / ID: 4nm5
TitleCrystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif
Components
  • Axin-1AXIN1
  • GSK3B proteinGlycogen synthase kinase-3 beta
  • Phosphorylated Wnt receptor LRP6 c-motif
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / phosphorylated Wnt receptor LRP6 c-motif / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


regulation of cellular component organization / Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / head development / cell development ...regulation of cellular component organization / Wnt signaling pathway involved in somitogenesis / Wnt-Frizzled-LRP5/6 complex / armadillo repeat domain binding / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Signaling by RNF43 mutants / neural crest formation / receptor-mediated endocytosis involved in cholesterol transport / head development / cell development / kinase inhibitor activity / Wnt receptor activity / low-density lipoprotein particle receptor activity / negative regulation of smooth muscle cell apoptotic process / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / dorsal/ventral axis specification / toxin transmembrane transporter activity / negative regulation of mesenchymal stem cell differentiation / 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 / Wnt-protein binding / midbrain dopaminergic neuron differentiation / cellular response to cholesterol / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / beta-catenin destruction complex disassembly / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / positive regulation of ubiquitin-dependent protein catabolic process / post-anal tail morphogenesis / negative regulation of protein acetylation / negative regulation of protein serine/threonine kinase activity / epigenetic programming in the zygotic pronuclei / tau-protein kinase / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / dopaminergic neuron differentiation / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / 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 / neural crest cell differentiation / negative regulation of protein metabolic process / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of protein localization to nucleus / glycogen metabolic process / nucleocytoplasmic transport / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / negative regulation of fat cell differentiation / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / tau-protein kinase activity / regulation of axonogenesis / establishment of cell polarity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / ER overload response / regulation of neuron projection development / negative regulation of developmental process / negative regulation of transcription elongation by RNA polymerase II / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / activation of protein kinase activity / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / R-SMAD binding / canonical Wnt signaling pathway / ubiquitin ligase-substrate adaptor activity / NF-kappaB binding / Regulation of HSF1-mediated heat shock response / lateral plasma membrane / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation
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 / 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 / Low density lipoprotein receptor-related protein 5/6 / 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 / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / 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 / 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 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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 c-motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,53511
Polymers46,6553
Non-polymers8808
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-66 kcal/mol
Surface area17830 Å2
MethodPISA
2
A: GSK3B protein
B: Axin-1
C: Phosphorylated Wnt receptor LRP6 c-motif
hetero molecules

A: GSK3B protein
B: Axin-1
C: Phosphorylated Wnt receptor LRP6 c-motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,07022
Polymers93,3116
Non-polymers1,75916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area12720 Å2
ΔGint-118 kcal/mol
Surface area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.727, 81.727, 280.937
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-580-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GSK3B protein / Glycogen synthase kinase-3 beta / 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 / 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
Details: Modified pGEX-KG / Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN1, AXIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O15169
#3: Protein/peptide Phosphorylated Wnt receptor LRP6 c-motif


Mass: 1060.141 Da / Num. of mol.: 1 / Fragment: Residues 1568-1575
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 , 5 types, 129 molecules

#4: 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
#5: 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
#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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
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: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 19, 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→39.24 Å / Num. all: 25689 / Num. obs: 25685 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 56.74 Å2 / Rsym value: 0.141 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.3818.114407924303.62699.6
7655

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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
Blu-Icedata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM7
Resolution: 2.3→39.237 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8334 / SU ML: 0.31 / σ(F): 1.91 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1283 5.01 %RANDOM
Rwork0.1826 ---
obs0.185 25608 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.4 Å2 / Biso mean: 70.3538 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 54 121 3192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023179
X-RAY DIFFRACTIONf_angle_d0.6314341
X-RAY DIFFRACTIONf_chiral_restr0.043488
X-RAY DIFFRACTIONf_plane_restr0.003557
X-RAY DIFFRACTIONf_dihedral_angle_d11.3741181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.39220.29681400.28992594273499
2.3922-2.50110.321620.270126152777100
2.5011-2.63290.34231340.241326612795100
2.6329-2.79780.28911420.215226392781100
2.7978-3.01380.27191400.215826822822100
3.0138-3.31690.28581180.203626992817100
3.3169-3.79660.21541340.17012717285199
3.7966-4.78190.18641560.144227712927100
4.7819-39.24260.21181570.17342947310499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.01430.640.22235.27530.50444.3236-0.2517-0.4030.71280.1620.1470.269-0.39890.10720.09670.6567-0.14820.1480.7387-0.04270.5355-15.732246.2883.931
24.4416-0.8191-1.17063.07912.86163.1351-0.0370.43940.1908-0.0569-0.11550.8219-0.0711-0.41710.06240.5369-0.1329-0.00660.73010.10970.6153-18.493341.6022-5.9427
34.74380.4591-0.27943.4294-0.22253.06390.0707-0.2481-0.0670.1699-0.0241-0.00170.25-0.2092-0.03140.397-0.0161-0.05180.3518-0.00820.3408-5.400633.4317-14.6819
42.72180.2879-0.13771.9829-0.79335.13670.0695-0.0703-0.4859-0.13220.06150.09670.70060.011-0.10720.5523-0.0213-0.09010.3216-0.06050.4976-3.27827.0177-24.8249
52.02261.3209-1.24826.2059-0.61288.31140.5940.94450.6703-0.9636-0.30950.1922-0.62690.2137-0.33270.8321-0.0671-0.04440.5040.01380.5276-4.685443.3721-44.2971
61.52512.586-1.96417.06030.06836.81770.3147-0.36360.81210.20660.0214-0.7146-0.6612-0.3398-0.30770.93530.1684-0.17441.2427-0.08681.2142-20.454344.7207-22.8892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 24:90A24 - 90
2X-RAY DIFFRACTION2chain A and resseq 91:136A91 - 136
3X-RAY DIFFRACTION3chain A and resseq 137:218A137 - 218
4X-RAY DIFFRACTION4chain A and resseq 219:383A219 - 389
5X-RAY DIFFRACTION5chain BB383 - 401
6X-RAY DIFFRACTION6chain CC6 - 11

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