8vmg

Crystal structure of GSK-3 26-383 bound to Axin 383-435

Method: X-RAY DIFFRACTION D_max: 115.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycogen synthase kinase-3 beta

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–383	Not recorded	Axin-1 × 1 （O15169） ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 20 NO3 NITRATE ION × 8 GOL GLYCEROL × 4 SO4 SULFATE ION × 7 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 26–383	Not recorded	Axin-1 × 1 （O15169） EDO 1,2-ETHANEDIOL × 19 SO4 SULFATE ION × 2 CL CHLORIDE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8VMG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NU1 Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide Deposited 2013-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–383（383 aa） Fragment：Residues 1-383 with phosphoylated Ser9	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris pH7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.50 Å R-free 0.245
5AIR Structural analysis of mouse GSK3beta fused with LRP6 peptide. Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–420（417 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ; Chain B 4–420（417 aa） Fragment：;RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420,RESIDUES 1565-1574, KINASE DOMAIN, RESIDUES 6-420 ;	Not recorded	MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；200 MM SODIUM MALONATE, 20 % (V/V) PEG 3350, pH 7	Resolution 2.53 Å R-free 0.260
6AE3 Crystal structure of GSK3beta complexed with Morin Deposited 2018-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–420（420 aa） Chain B 1–420（420 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MRI 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；100mM Sodium Citrate (pH6.5), 18%(v/v) PEG 4000, 5%(v/v) 2-propanol	Resolution 2.14 Å R-free 0.226
6AE3 Crystal structure of GSK3beta complexed with Morin Deposited 2018-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–420（420 aa） Chain D 1–420（420 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；100mM Sodium Citrate (pH6.5), 18%(v/v) PEG 4000, 5%(v/v) 2-propanol	Resolution 2.14 Å R-free 0.226
8VME Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide Deposited 2024-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–383（358 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 6 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 200 uM ATP, 5 mM DTT	Resolution 2.30 Å R-free 0.230
8VMF Crystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide Deposited 2024-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–383（358 aa）	Not recorded	MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG35000, 20 mM Tris, pH 7.5, 300 mM sodium chloride, 5% glycerol, 10 mM magnesium chloride, 5 mM DTT, 200 uM ADP, 200 uM aluminum nitrate, 1.2 mM sodium fluoride	Resolution 2.50 Å R-free 0.251

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSK3B_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–358； UniProt 26–383 Author chain B； PDBConstruct 1–358； UniProt 26–383

Axin-1

Homo sapiens

UniProt O15169

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 383–435	Not recorded	Glycogen synthase kinase-3 beta × 1 （Q9WV60） ADP ADENOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 20 NO3 NITRATE ION × 8 GOL GLYCEROL × 4 SO4 SULFATE ION × 7 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 383–435	Not recorded	Glycogen synthase kinase-3 beta × 1 （Q9WV60） EDO 1,2-ETHANEDIOL × 19 SO4 SULFATE ION × 2 CL CHLORIDE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM MES, pH 5.5, 1.9 M ammonium sulfate, 200 mM sodium chloride, cryoprotectant: 25% ethylene glycol	Resolution 2.45 Å R-free 0.230

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8VMG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DK8 CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN Deposited 1999-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 111–257（147 aa） Fragment：RGS-HOMOLOGOUS DOMAIN	Not recorded	SO4 SULFATE ION × 12 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.25；277 K；sodium acetate, ammonium sulfate, glycerol, dithiothreitol, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.57 Å R-free 0.198
1EMU STRUCTURE OF THE AXIN RGS-HOMOLOGOUS DOMAIN IN COMPLEX WITH A SAMP REPEAT FROM APC Deposited 2000-03-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 117–248（132 aa） Fragment：RGS-HOMOLOGOUS DOMAIN	Not recorded	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；MES, PEG 400, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.221
1O9U GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH AXIN PEPTIDE Deposited 2002-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	ADZ 9-METHYL-9H-PURIN-6-AMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTAL WERE GROWN BY THE HANGING DROP METHOD. 1UL OF PROTEIN SOLUTION (6MG/ML GSK3B AND 0.37MG/ML AXIN PEPTIDE) IN 25MM HEPES-NAOH, 250MM NACL, 1MM DTT, PH 7.0) WAS MIXED WITH 1UL PRECIPITANT (18% PEG4000, 150MM MGCL2, 100MM TRIS- HCL, PH 7.5)	Resolution 2.40 Å R-free 0.260
3ZDI Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Inhibitor 7d Deposited 2012-11-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	PO4 PHOSPHATE ION × 1 UGJ 3,6-Diamino-4-(2-chlorophenyl)thieno[2,3-b]pyridine-2,5-dicarbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES), PH 6.5, 12% (W/V) PEG 20000	Resolution 2.65 Å R-free 0.242
4B7T Glycogen Synthase Kinase 3 Beta complexed with Axin Peptide and Leucettine L4 Deposited 2012-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–400（18 aa） Fragment：RESIDUES 383-400	Not recorded	CWT (5Z)-5-(1,3-benzodioxol-5-ylmethylidene)-3-methyl-2-(propan-2-ylamino)imidazol-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M TRIS-HCL, PH 8.0, 0.15 M MGCL2, 15% (W/V) PEG 4000	Resolution 2.77 Å R-free 0.235
4NM0 Crystal structure of peptide inhibitor-free GSK-3/Axin complex Deposited 2013-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 20mM MgCl2, 400uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.50 Å R-free 0.239
4NM3 Crystal structure of GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide Deposited 2013-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.10 Å R-free 0.242
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232
4NM5 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif Deposited 2013-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 8 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.232
4NM7 Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif Deposited 2013-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；277 K；10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.30 Å R-free 0.234
4NU1 Crystal structure of a transition state mimic of the GSK-3/Axin complex bound to phosphorylated N-terminal auto-inhibitory pS9 peptide Deposited 2013-12-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 383–402（20 aa） Fragment：Residues 383-402	Not recorded	GOL GLYCEROL × 2 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；277 K；10% PEG 35,000, 20mM Tris pH7.5, 300mM NaCl, 5% glycerol, 10mM MgCl2, 200uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K	Resolution 2.50 Å R-free 0.245
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
5WZZ The SIAH E3 ubiquitin ligases promote Wnt/ beta-catenin signaling through mediating Wnt-induced Axin degradation Deposited 2017-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 375–394（20 aa） Fragment：UNP residues 375-394	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；25% (w/v) PEG3350, 200 mM MgCl2, 100 mM Tris-Hcl	Resolution 2.10 Å R-free 0.208
6JCK Complex structure of Axin-DIX and Dvl2-DIX Deposited 2019-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 745–826（82 aa）	Mutation：Y760D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；25% (w/v) PEG1500, 0.1 M Malonate-Imidazole-Borate buffer pH 7.0	Resolution 3.09 Å R-free 0.290
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	I5L (2~{Z},4~{Z})-2-methyl-5-(8-oxidanyldibenzofuran-4-yl)penta-2,4-dienal × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
7Y1P CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na Deposited 2022-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 74–220（147 aa） Fragment：RGS-homologous domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；2.4 M sodium malonate pH 7.0	Resolution 2.60 Å R-free 0.228
8RU3 Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor Deposited 2024-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 468–479（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；300 K；Crystals grown in 100 mM NaKPO4, 2M NaCl.	Resolution 2.00 Å R-free 0.232
8RU4 Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor Deposited 2024-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 469–479（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GLC alpha-D-glucopyranose × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；100 mM TRIS pH 8.75, 2%(w/v) PEG-6000, cryoprotected in 30% (w/v) Glucose.	Resolution 2.13 Å R-free 0.240

15 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AXIN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 8–60； UniProt 383–435 Author chain D； PDBConstruct 8–60； UniProt 383–435

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8vmg
Deposition date deposition_date	2024-01-13
Structure title title	Crystal structure of GSK-3 26-383 bound to Axin 383-435
Keywords keywords	GSK-3, kinase, TRANSFERASE-SIGNALING PROTEIN complex; TRANSFERASE/SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.37 Å
Radius of gyration Rg (electron density) rg_electron	31.73 Å
Forward intensity I(0) i0	137075000.00
Molecular weight molecular_weight	91795.0 kDa
Excluded volume excluded_volume	114340 Å³
Envelope volume envelope_volume	147730 Å³
Hydration-shell volume shell_volume	39551 Å³
Envelope diameter envelope_diameter	125.5 Å
Shell Rg shell_rg	37.68 Å
Envelope Rg envelope_rg	32.32 Å
Shape Rg shape_rg	31.71 Å
Total Rg total_rg	32.27 Å
Total atoms total_atoms	6682
Residues n_residues	778
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.6 Å
Rg (real space) rg_real	32.49 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	1.3710e+08
I(0) uncertainty (real space) i0_real_error	2.3580e+06
Rg (reciprocal space) rg_reciprocal	32.44 Å
I(0) (reciprocal space) i0_reciprocal	137100000.0000
Solution quality estimate total_estimate	0.8484
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.468
Kurtosis Kurtosis kurtosis	-0.151
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35790000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.909

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Glycogen synthase kinase-3 beta
Molecular weight formula_weight	41538.7 kDa
EC 编号 ec_number	2.7.11.26,2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6951

MKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Axin-1
Molecular weight formula_weight	6657.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GGWGSGGVEPQKFAEELIHRLEAVQRTREAEEKLEERLKRVRMEEEGEDGDPSSGPPGPC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	39

Entity 5 Entity 5 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 10 Entity 10 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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8. Citations (1)

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Unit-cell length a length_a	195.585 Å
Unit-cell length b length_b	195.585 Å
Unit-cell length c length_c	152.204 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	39.760 Å
R factor r_factor	0.1953
R_work r_work	0.1947
R_free r_free	0.2301

fit	/app/data/saxs_computation/vm/8vmg/8vmg.fit
pddf	/app/data/pr_computation/vm/8vmg/8vmg.pr.out
profile	/app/data/saxs_computation/vm/8vmg/8vmg.dat

Crystal structure of GSK-3 26-383 bound to Axin 383-435

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycogen synthase kinase-3 beta

State in the Current Structure

Other States of the Same Protein in the Database

Axin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)