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- PDB-9i8x: Beta-catenin armadillo with cyclic peptide and Compound 2 -

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Basic information

Entry
Database: PDB / ID: 9i8x
TitleBeta-catenin armadillo with cyclic peptide and Compound 2
Components
  • Catenin beta-1
  • Cyclic peptide
KeywordsONCOPROTEIN / Beta-catenin / complex / 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 / beta-catenin-TCF complex / Specification of the neural plate border / neuron fate determination / 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 / layer formation in cerebral cortex / mesenchymal to epithelial transition / hindbrain development / presynaptic active zone cytoplasmic component / fungiform papilla formation / positive regulation of determination of dorsal identity / regulation of protein localization to cell surface / fascia adherens / positive regulation of skeletal muscle tissue development / 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 / establishment of blood-brain barrier / Formation of axial mesoderm / beta-catenin destruction complex / midbrain dopaminergic neuron differentiation / 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
~{N}-(4-bromophenyl)ethanamide / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 2
Authors: Klejnot, M. / Skowron, A.N. / Pastok, M.W. / Gorecka-Minakowska, K.M. / Wisniewski, J. / Walczak, M.J.
History
DepositionFeb 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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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)61,3499
Polymers60,5592
Non-polymers7907
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-92 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 90.940, 120.340
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-IJX / ~{N}-(4-bromophenyl)ethanamide


Mass: 214.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8BrNO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-TRIS pH 6.5, 0.2 M Lithium sulfate monohydrate, 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.98→47.4 Å / Num. obs: 39292 / % possible obs: 97.1 % / Redundancy: 7.94 % / CC1/2: 0.998 / Net I/σ(I): 6.69
Reflection shellResolution: 1.98→2.1 Å / Num. unique obs: 5333 / CC1/2: 0.014

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.47 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.06 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28596 1935 5 %RANDOM
Rwork0.21805 ---
obs0.22147 36753 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.084 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å2-0 Å20 Å2
2---2.12 Å2-0 Å2
3---4.16 Å2
Refinement stepCycle: 1 / Resolution: 2→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 30 40 4085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124096
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164072
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6595562
X-RAY DIFFRACTIONr_angle_other_deg0.4911.5769329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.1676.550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86410708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
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_it4.6655.5442034
X-RAY DIFFRACTIONr_mcbond_other4.6645.5442034
X-RAY DIFFRACTIONr_mcangle_it6.1129.9632539
X-RAY DIFFRACTIONr_mcangle_other6.1119.9652540
X-RAY DIFFRACTIONr_scbond_it6.8056.462062
X-RAY DIFFRACTIONr_scbond_other6.6396.4122039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5711.4552988
X-RAY DIFFRACTIONr_long_range_B_refined11.43555.764619
X-RAY DIFFRACTIONr_long_range_B_other11.43455.764620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.542 131 -
Rwork0.518 2491 -
obs--92.49 %

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