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8vmf

Crystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide

Method: X-RAY DIFFRACTION Dmax: 77.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycogen synthase kinase-3 beta

Mus musculus

UniProt Q9WV60

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 26–383 Not recorded Axin-1 × 1 （O35625） Catenin beta-1 × 1 （P35222） 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

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 8VMF 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 oligomeric state 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 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
8VMG Crystal structure of GSK-3 26-383 bound to Axin 383-435 Deposited 2024-01-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–383（358 aa）
Not recorded 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
8VMG Crystal structure of GSK-3 26-383 bound to Axin 383-435 Deposited 2024-01-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–383（358 aa）
Not recorded 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

5 other PDB entries and 7 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

Axin-1

Homo sapiens

UniProt O35625

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 383–402 Not recorded Glycogen synthase kinase-3 beta × 1 （Q9WV60） Catenin beta-1 × 1 （P35222） 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

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 8VMF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3UTM Crystal structure of a mouse Tankyrase-Axin complex Deposited 2011-11-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–80（80 aa） Fragment：mAxin1 N domain (UNP Residues 1-80)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.6；295 K；0.06 M sodium citrate tribasic dihydrate pH 5.6, 1.2M ammonium acetate, 18% MPD, and 20mM DTT, EVAPORATION, temperature 295K
Resolution 2.00 Å R-free 0.238
8VME Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide Deposited 2024-01-13 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）
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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AXIN1_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–24； UniProt 383–402

Catenin beta-1

Homo sapiens

UniProt P35222

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 35–61 Mutation：S45D Glycogen synthase kinase-3 beta × 1 （Q9WV60） Axin-1 × 1 （O35625） 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

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 8VMF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1G3J CRYSTAL STRUCTURE OF THE XTCF3-CBD/BETA-CATENIN ARMADILLO REPEAT COMPLEX Deposited 2000-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 133–664（532 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；2.5% PEG-8000, 44mM Phosphate-Citrate, 2mM DTT, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.255
1G3J CRYSTAL STRUCTURE OF THE XTCF3-CBD/BETA-CATENIN ARMADILLO REPEAT COMPLEX Deposited 2000-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 133–664（532 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；2.5% PEG-8000, 44mM Phosphate-Citrate, 2mM DTT, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.10 Å R-free 0.255
1JDH CRYSTAL STRUCTURE OF BETA-CATENIN AND HTCF-4 Deposited 2001-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 135–663（529 aa） Fragment：Residues 135-663
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.231
1JPW Crystal Structure of a Human Tcf-4 / beta-Catenin Complex Deposited 2001-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 131–670（540 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；PEG 400, MES, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22K
Resolution 2.50 Å R-free 0.390
1JPW Crystal Structure of a Human Tcf-4 / beta-Catenin Complex Deposited 2001-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 131–670（540 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；PEG 400, MES, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22K
Resolution 2.50 Å R-free 0.390
1JPW Crystal Structure of a Human Tcf-4 / beta-Catenin Complex Deposited 2001-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 131–670（540 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；PEG 400, MES, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22K
Resolution 2.50 Å R-free 0.390
1LUJ Crystal Structure of the Beta-catenin/ICAT Complex Deposited 2002-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 150–663（514 aa） Fragment：residues 150-666
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG800, magnesium chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.255
1P22 Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase Deposited 2003-04-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 19–44（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.286
1QZ7 Beta-catenin binding domain of Axin in complex with beta-catenin Deposited 2003-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 133–665（533 aa） Fragment：Armadillo repeat region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；PEG 6000, sodium citrate, isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.256
1T08 Crystal structure of beta-catenin/ICAT helical domain/unphosphorylated APC R3 Deposited 2004-04-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 146–664（519 aa） Fragment：armadillo repeat (RESIDUES 146-664)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；297 K；PEG3400, Potassium phosphate, pH 6.5, EVAPORATION, temperature 297K
Resolution 2.10 Å R-free 0.241
1TH1 Beta-catenin in complex with a phosphorylated APC 20aa repeat fragment Deposited 2004-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 133–664（532 aa） Fragment：armadillo repeat
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tris, sidium chloride, PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.257
1TH1 Beta-catenin in complex with a phosphorylated APC 20aa repeat fragment Deposited 2004-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 133–664（532 aa） Fragment：armadillo repeat
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Tris, sidium chloride, PEG2000MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.257
2G57 Structure of the Phosphorylation Motif of the oncogenic Protein beta-Catenin Recognized By a Selective Monoclonal Antibody Deposited 2006-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–44（26 aa） Fragment：Residues 19-44
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；278 K；Ionic strength (raw mmCIF value) 20mM；Pressure 1
NMR sample composition 1mM P-beta-Cat peptide with 0.01mM antibody; 20mM phosphate buffered saline(pH 7.4); 15mM sodium azide; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2GL7 Crystal Structure of a beta-catenin/BCL9/Tcf4 complex Deposited 2006-04-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 138–686（549 aa） Fragment：Residues 138-686
Mutation：Y142E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13% PEG 3350, 125mM sodium thiocyanate, 5% Glycerol, 10mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.267
2GL7 Crystal Structure of a beta-catenin/BCL9/Tcf4 complex Deposited 2006-04-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 138–686（549 aa） Fragment：Residues 138-686
Mutation：Y142E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13% PEG 3350, 125mM sodium thiocyanate, 5% Glycerol, 10mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.267
2Z6H Crystal Structure of Beta-Catenin Armadillo Repeat Region and Its C-Terminal domain Deposited 2007-08-01 Different construct Different mutation/modification 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 138–781（644 aa） Fragment：Armadillo Repeat Region and C-terminal Domain (UNP residues 138-781)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1M Na Citrate, 0.4M NaCl, 7% JEFFAMINE ED-2001, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
2Z6H Crystal Structure of Beta-Catenin Armadillo Repeat Region and Its C-Terminal domain Deposited 2007-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 138–781（644 aa） Fragment：Armadillo Repeat Region and C-terminal Domain (UNP residues 138-781)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1M Na Citrate, 0.4M NaCl, 7% JEFFAMINE ED-2001, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
3DIW c-terminal beta-catenin bound TIP-1 structure Deposited 2008-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 772–781（10 aa） Fragment：C-terminal domain, UNP residues 772-781
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.0M sodium formate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.265
3DIW c-terminal beta-catenin bound TIP-1 structure Deposited 2008-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 772–781（10 aa） Fragment：C-terminal domain, UNP residues 772-781
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；3.0M sodium formate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.265
3SL9 X-ray structure of Beta catenin in complex with Bcl9 Deposited 2011-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 141–305（165 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 2 IMD IMIDAZOLE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
3SL9 X-ray structure of Beta catenin in complex with Bcl9 Deposited 2011-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 141–305（165 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 IMD IMIDAZOLE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
3SL9 X-ray structure of Beta catenin in complex with Bcl9 Deposited 2011-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 141–305（165 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 IMD IMIDAZOLE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
3SL9 X-ray structure of Beta catenin in complex with Bcl9 Deposited 2011-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 141–305（165 aa）
Not recorded IMD IMIDAZOLE × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.249
3SLA X-ray structure of first four repeats of human beta-catenin Deposited 2011-06-24 Different construct Different mutation/modification 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 141–306（166 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.277
3SLA X-ray structure of first four repeats of human beta-catenin Deposited 2011-06-24 Different construct Different mutation/modification 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 141–306（166 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.277
3SLA X-ray structure of first four repeats of human beta-catenin Deposited 2011-06-24 Different construct Different mutation/modification 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 141–306（166 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.277
3SLA X-ray structure of first four repeats of human beta-catenin Deposited 2011-06-24 Different construct Different mutation/modification 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 141–306（166 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.277
3SLA X-ray structure of first four repeats of human beta-catenin Deposited 2011-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 141–306（166 aa）
Not recorded GOL GLYCEROL × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.277
3TX7 Crystal structure of LRH-1/beta-catenin complex Deposited 2011-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 138–663（526 aa）
Not recorded P6L (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；20 mM Tris-HCl, 40% PEG200, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.76 Å R-free 0.243
4DJS Structure of beta-catenin in complex with a stapled peptide inhibitor Deposited 2012-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 148–665（518 aa） Fragment：armadillo repeats 1-12 (UNP residues 148-665)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；1.4-2.0 M sodium chloride, 100 mM Bis-Tris, 100 mM potassium phosphate monobasic, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.03 Å R-free 0.291
6M90 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex Deposited 2018-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 17–48（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) J91 2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.05 Å R-free 0.212
6M91 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex Deposited 2018-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 17–48（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) J97 3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.40 Å R-free 0.216
6M92 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex Deposited 2018-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 17–48（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) J8V 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.35 Å R-free 0.221
6M93 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex Deposited 2018-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 17–48（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) J8Y 2-oxo-N-[3-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.50 Å R-free 0.230
6M94 Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex Deposited 2018-08-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 17–48（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH5.5
Resolution 2.70 Å R-free 0.238
6O9B Crystal structure of HLA-A3*01 in complex with a wild-type beta-catenin peptide Deposited 2019-03-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 41–49（9 aa） Fragment：UNP residues 41-49
Not recorded PG4 TETRAETHYLENE GLYCOL × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 IMD IMIDAZOLE × 2 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M MES/imidazole, pH 6.5, 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol, 20% PEG500 MME, 10% PEG20000
Resolution 2.20 Å R-free 0.227
6O9C Crystal structure of HLA-A3*01 in complex with a mutant beta-catenin peptide Deposited 2019-03-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 41–49（9 aa） Fragment：UNP residues 41-49
Mutation：S45F MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 10 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M MES, pH 6.5, 0.2 M ammonium sulfate, 30% PEG5000 MME
Resolution 2.45 Å R-free 0.259
6WLX PAK4 kinase domain in complex with beta-catenin Ser675 substrate peptide Deposited 2020-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 671–677（7 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；0.1M Tris-HCl, 2M Na acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, 5mM peptide
Resolution 2.20 Å R-free 0.229
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 31–39（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 31–39（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 31–39（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
7AFW Beta-Catenin in complex with compound 6 Deposited 2020-09-21 Different construct Different mutation/modification 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 141–305（165 aa）
Not recorded R9Q 3-[(2~{R})-4-methyl-5-oxidanylidene-2,3-dihydro-1,4-benzoxazepin-2-yl]benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；278 K；25% PEG 3350, 100 mM BIS-TRIS buffer pH 5.5 and 0.2 M Magnesium chloride
Resolution 1.81 Å R-free 0.281
7AR4 Crystal structure of beta-catenin in complex with cyclic peptide inhibitor Deposited 2020-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 134–665（532 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M HEPES, 4% PEG6000, 20 mM TRIS, 150 mM NaCl, 0.5 % Glycerol, 2 mM DTT
Resolution 2.60 Å R-free 0.242
7UWI Structure of beta-catenin in complex with FP01567, a Helicon Polypeptide Deposited 2022-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 143–663（521 aa）
Not recorded PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 6 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M Sodium phosphate monobasic monohydrate, 0.1 M Potassium phosphate monobasic, 0.1 M MES monohydrate pH 6.5, 2.0 M Sodium chloride
Resolution 2.32 Å R-free 0.278
7UWO Structure of beta-catenin in complex with FP05874, a Helicon Polypeptide Deposited 2022-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–665（532 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.05M MgCl2, 0.1M MES pH6.5, 5% (w/v) PEG 4000
Resolution 2.75 Å R-free 0.253
8EI9 Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H332, a Helicon Polypeptide Deposited 2022-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 134–665（532 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES Sodium Salt pH6.5, 10% v/v 2-Propanol, 25% v/v PEG 400
Resolution 3.90 Å R-free 0.315
8EIA Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H333, a Helicon Polypeptide Deposited 2022-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 134–665（532 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Potassium chloride, 0.1 M HEPES pH 7, 15% w/v PEG 5000 MME
Resolution 3.60 Å R-free 0.373
8EIB Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H329, a Helicon Polypeptide Deposited 2022-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 134–665（532 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M Calcium acetate pH 7.5, 20% w/v PEG 3350
Resolution 3.76 Å R-free 0.298
8EIC Crystal structure of beta-catenin and the MDM2 p53-binding domain in complex with H330, a Helicon Polypeptide Deposited 2022-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 134–665（532 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；4M Sodium formate
Resolution 2.62 Å R-free 0.269
8RU3 Crystal structure of beta-catenin in complex with alpha-helical peptide inhibitor Deposited 2024-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–665（532 aa）
Not recorded 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 145–665（521 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
8RU4 Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor Deposited 2024-01-30 Different construct Different mutation/modification 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 145–665（521 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GLC alpha-D-glucopyranose × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 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
8VME Crystal structure of the GSK-3/Axin complex bound to a phosphorylated beta-catenin T41A peptide Deposited 2024-01-13 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 35–61（27 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
8Y0G Human beta-catenin crystal structure Deposited 2024-01-22 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Apo crystals of beta-Catenin were grown from 14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline Crystal were transferred into soaking solution and incubated at RT for 1 days. Crystals were transferred into cryoprotectant (14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol), and then flash frozen in liquid nitrogen.
Resolution 2.50 Å R-free 0.287
8Y0P Beta-Catenin in complex with peptide 301 Deposited 2024-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 138–686（549 aa）
Not recorded PRO PROLINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；14% PEG 3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol
Resolution 2.62 Å R-free 0.279
8Y0P Beta-Catenin in complex with peptide 301 Deposited 2024-01-22 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；14% PEG 3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol
Resolution 2.62 Å R-free 0.279
8Y14 Beta-catenin Crystal Structure Deposited 2024-01-23 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；14% PEG 3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol
Resolution 2.80 Å R-free 0.264
8Z0U Human beta-catenin crystal structure Deposited 2024-04-10 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Apo crystals of beta-Catenin were grown from 14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline. Crystal were transferred into soaking solution and incubated at RT for 4 days. Crystals were transferred into cryoprotectant (14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol), and then flash frozen in liquid nitrogen.
Resolution 2.21 Å R-free 0.281
8Z10 Human beta-catenin crystal structure Deposited 2024-04-10 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded PRO PROLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Apo crystals of beta-Catenin were grown from 14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline. Crystal was transferred into a soaking solution and incubated at RT for 4 days. Crystals were transferred into cryoprotectant (14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol), and then flash frozen in liquid nitrogen.
Resolution 2.35 Å R-free 0.275
8Z5J Beta-catenin Crystal Structure Deposited 2024-04-18 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；14% PEG 3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol
Resolution 2.80 Å R-free 0.264
8Z61 Human beta-catenin crystal structure Deposited 2024-04-18 Different construct Different mutation/modification 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 138–686（549 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Apo crystals of beta-Catenin were grown from 14% PEG 3350, 0.1M Hepes pH 7.5, 0.2M L-proline (Crystal were transferred into soaking solution and incubated at RT for 1 days. Crystals were transferred into cryoprotectant (14% PEG3350, 0.1M Hepes pH 7.5, 0.2M L-proline, 20% glycerol), and then flash frozen in liquid nitrogen.)
Resolution 2.50 Å R-free 0.287
9I8K Beta-catenin armadillo (150-663) Deposited 2025-02-05 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 150–663（514 aa）
Chain B 150–663（514 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Buffer system 1 pH 6.5, 0.12 M monosaccharides mix, 50% precipitant mix 4
Resolution 2.00 Å R-free 0.239
9I8W Beta-catenin armadillo with cyclic peptide and Compound 3 Deposited 2025-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–671（538 aa）
Not recorded HHT 2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M ADA pH 6.5, 100 mM ammonium sulfate, 30 % w/v PEG MME 5000
Resolution 2.20 Å R-free 0.244
9I8X Beta-catenin armadillo with cyclic peptide and Compound 2 Deposited 2025-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 134–671（538 aa）
Not recorded IJX ~{N}-(4-bromophenyl)ethanamide × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-TRIS pH 6.5, 0.2 M Lithium sulfate monohydrate, 26% PEG 3350
Resolution 2.00 Å R-free 0.286

46 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTNB1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–28； UniProt 35–61

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

SAXS profile for 8vmf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vmf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vmf
Deposition date deposition_date2024-01-13
Structure title titleCrystal structure of a transition-state mimic of the GSK-3/Axin complex bound to a beta-catenin S45D peptide
Keywords keywordsGSK-3, kinase, TRANSFERASE-SIGNALING PROTEIN complex; TRANSFERASE/SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.89 Å
Radius of gyration Rg (electron density) rg_electron21.80 Å
Forward intensity I(0) i030718100.00
Molecular weight molecular_weight42969.0 kDa
Excluded volume excluded_volume53998 ų
Envelope volume envelope_volume64082 ų
Hydration-shell volume shell_volume24462 ų
Envelope diameter envelope_diameter80.2 Å
Shell Rg shell_rg28.88 Å
Envelope Rg envelope_rg22.29 Å
Shape Rg shape_rg21.81 Å
Total Rg total_rg22.67 Å
Total atoms total_atoms3049
Residues n_residues379
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.5 Å
Rg (real space) rg_real22.84 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.0720e+07
I(0) uncertainty (real space) i0_real_error3.7880e+05
Rg (reciprocal space) rg_reciprocal22.85 Å
I(0) (reciprocal space) i0_reciprocal30720000.0000
Solution quality estimate total_estimate0.6864
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.2 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.270
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8223000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 0.171; Positv: 1.000; Valcen: 0.996; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)