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- PDB-2bct: THE ARMADILLO REPEAT REGION FROM MURINE BETA-CATENIN -

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Basic information

Entry
Database: PDB / ID: 2bct
TitleTHE ARMADILLO REPEAT REGION FROM MURINE BETA-CATENIN
ComponentsBETA-CATENIN
KeywordsSTRUCTURAL PROTEIN / ARMADILLO REPEAT / BETA-CATENIN
Function / homology
Function and homology information


lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / hair cycle process ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / hair cycle process / positive regulation of epithelial cell differentiation / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / trachea morphogenesis / mesenchyme development / endoderm formation / Formation of the beta-catenin:TCF transactivating complex / VEGFR2 mediated vascular permeability / 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 / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of timing of anagen / Ca2+ pathway / central nervous system vasculogenesis / animal organ development / regulation of epithelial cell differentiation / Schwann cell proliferation / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / Degradation of beta-catenin by the destruction complex / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / delta-catenin binding / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / cranial skeletal system development / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / presynaptic active zone cytoplasmic component / smooth muscle cell differentiation / cell projection membrane / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / mesenchymal cell proliferation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / male genitalia development
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuber, A.H. / Nelson, W.J. / Weis, W.I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Three-dimensional structure of the armadillo repeat region of beta-catenin.
Authors: Huber, A.H. / Nelson, W.J. / Weis, W.I.
History
DepositionJul 30, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-CATENIN


Theoretical massNumber of molelcules
Total (without water)56,3141
Polymers56,3141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.090, 75.590, 134.420
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 BETA-CATENIN


Mass: 56314.336 Da / Num. of mol.: 1 / Fragment: ARMADILLO REPEAT REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5
Details: 10% (W/V) PEG 8000, 875 MM NACL, 200 MM TRIS-HCL, PH 8.5
Crystal grow
*PLUS
pH: 10.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlbeta-591drop
210 mMCAPS1drop
350 mM1dropNaCl
41 mMDTT1drop
510 %(w/v)PEG80001reservoir
6200 mMTris-HCl1reservoir
7875 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 11818 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 22.7
Reflection shellResolution: 2.9→3.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.257 / % possible all: 93.4
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BCT

3bct


Resolution: 2.9→40 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1178 10.4 %RANDOM
Rwork0.211 ---
obs0.211 11380 94 %-
Solvent computationSolvent model: X-PLOR/CNS / Bsol: 15.23 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--4.05 Å20 Å2
3----7.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 0 0 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.91.5
X-RAY DIFFRACTIONc_mcangle_it4.682
X-RAY DIFFRACTIONc_scbond_it4.642
X-RAY DIFFRACTIONc_scangle_it6.752.5
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 182 10.8 %
Rwork0.365 1507 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2

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