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- PDB-9i8w: Beta-catenin armadillo with cyclic peptide and Compound 3 -

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Basic information

Entry
Database: PDB / ID: 9i8w
TitleBeta-catenin armadillo with cyclic peptide and Compound 3
Components
  • Catenin beta-1
  • Cyclic peptide
KeywordsONCOPROTEIN / Beta-catenin armadillo / cyclic peptide
Function / homology
Function and homology information


canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex ...canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / regulation of secondary heart field cardioblast proliferation / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / embryonic skeletal limb joint morphogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / acinar cell differentiation / embryonic axis specification / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / neuron fate determination / beta-catenin-TCF complex / Specification of the neural plate border / synaptic vesicle clustering / endodermal cell fate commitment / Formation of the nephric duct / proximal/distal pattern formation / endothelial tube morphogenesis / dorsal root ganglion development / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal/ventral axis specification / sympathetic ganglion development / lung epithelial cell differentiation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / layer formation in cerebral cortex / positive regulation of skeletal muscle tissue development / mesenchymal to epithelial transition / hindbrain development / fungiform papilla formation / positive regulation of determination of dorsal identity / regulation of protein localization to cell surface / fascia adherens / positive regulation of myoblast proliferation / ectoderm development / embryonic foregut morphogenesis / detection of muscle stretch / positive regulation of odontoblast differentiation / smooth muscle cell differentiation / mesenchymal cell proliferation involved in lung development / hair cell differentiation / alpha-catenin binding / cellular response to indole-3-methanol / histone methyltransferase binding / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / epithelial cell proliferation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development / flotillin complex / cranial skeletal system development / cell-cell adhesion mediated by cadherin / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / lung-associated mesenchyme development / midbrain dopaminergic neuron differentiation / establishment of blood-brain barrier / Formation of axial mesoderm / beta-catenin destruction complex / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / catenin complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / embryonic brain development / gastrulation with mouth forming second / positive regulation of blood vessel branching / embryonic heart tube development / pancreas development
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKlejnot, M. / Skowron, A.N. / Pastok, M.W. / Gorecka-Minakowska, K.M. / Wisniewski, J. / Walczak, M.J.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Center for Research and Development (Poland)POIR.01.02.00-00-0073/18 Poland
CitationJournal: To Be Published
Title: Beta-catenin armadillo with cyclic peptide and Compound 3
Authors: Klejnot, M. / Skowron, A.N. / Pastok, M.W. / Gorecka-Minakowska, K.M. / Wisniewski, J. / Walczak, M.
History
DepositionFeb 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 2.0Apr 22, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / exptl_crystal_grow / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_conf / struct_conn / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _exptl_crystal_grow.pdbx_details ..._entity.pdbx_number_of_molecules / _exptl_crystal_grow.pdbx_details / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_high / _reflns.number_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle
Provider: author / Type: Coordinate replacement
Revision 2.1May 6, 2026Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0926
Polymers60,5592
Non-polymers5334
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-45 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.660, 90.470, 120.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 58844.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / References: UniProt: P35222
#2: Protein/peptide Cyclic peptide


Mass: 1714.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-HHT / 2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid


Mass: 245.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9BrO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ADA pH 6.5, 100 mM ammonium sulfate, 30 % w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→47.5 Å / Num. obs: 29416 / % possible obs: 99.7 % / Redundancy: 9.9 % / CC1/2: 0.998 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2524 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.93 / SU B: 18.339 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24436 1456 5 %RANDOM
Rwork0.18259 ---
obs0.1856 27919 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.985 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å2-0 Å20 Å2
2---3.62 Å2-0 Å2
3---5.88 Å2
Refinement stepCycle: 1 / Resolution: 2.2→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 0 148 60 4105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0124099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164081
X-RAY DIFFRACTIONr_angle_refined_deg2.6411.8255565
X-RAY DIFFRACTIONr_angle_other_deg0.8521.749351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.5556.91547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77910709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02880
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0394.2272042
X-RAY DIFFRACTIONr_mcbond_other5.0324.2282042
X-RAY DIFFRACTIONr_mcangle_it6.1827.5832549
X-RAY DIFFRACTIONr_mcangle_other6.1817.5852550
X-RAY DIFFRACTIONr_scbond_it7.3975.0162057
X-RAY DIFFRACTIONr_scbond_other7.234.9962044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.648.8712999
X-RAY DIFFRACTIONr_long_range_B_refined10.45342.994549
X-RAY DIFFRACTIONr_long_range_B_other10.45342.984546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.59 99 -
Rwork0.507 2045 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: -6.1258 Å / Origin y: -7.1523 Å / Origin z: 16.0103 Å
111213212223313233
T0.0501 Å20.0182 Å20.0169 Å2-0.0197 Å20.011 Å2--0.008 Å2
L1.5793 °21.3363 °20.3035 °2-1.3589 °20.1958 °2--0.3143 °2
S-0.0602 Å °0.1031 Å °0.0127 Å °-0.1269 Å °0.0697 Å °-0.0038 Å °-0.0324 Å °0.0025 Å °-0.0095 Å °

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