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- PDB-1dow: CRYSTAL STRUCTURE OF A CHIMERA OF BETA-CATENIN AND ALPHA-CATENIN -

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Basic information

Entry
Database: PDB / ID: 1dow
TitleCRYSTAL STRUCTURE OF A CHIMERA OF BETA-CATENIN AND ALPHA-CATENIN
Components
  • ALPHA-CATENIN
  • BETA-CATENIN
KeywordsCELL ADHESION / four-helix bundle
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 / negative regulation of integrin-mediated signaling pathway / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins ...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 / negative regulation of integrin-mediated signaling pathway / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins / Disassembly of the destruction complex and recruitment of AXIN to the membrane / hair cycle process / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / endoderm formation / mesenchyme development / trachea morphogenesis / Formation of the beta-catenin:TCF transactivating complex / positive regulation of epithelial cell differentiation / Deactivation of the beta-catenin transactivating complex / 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 / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / animal organ development / 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 / VEGFR2 mediated vascular permeability / regulation of epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / Degradation of beta-catenin by the destruction complex / Adherens junctions interactions / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / gamma-catenin binding / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / epithelial cell-cell adhesion / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / zonula adherens / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / gap junction assembly / fungiform papilla formation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / mesenchymal cell proliferation / alpha-catenin binding / cranial skeletal system development / regulation of calcium ion import
Similarity search - Function
Alpha-catenin / Beta-catenin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat ...Alpha-catenin / Beta-catenin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Catenin alpha-1 / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPokutta, S. / Weis, W.I.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure of the dimerization and beta-catenin-binding region of alpha-catenin.
Authors: Pokutta, S. / Weis, W.I.
History
DepositionDec 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-CATENIN
B: BETA-CATENIN


Theoretical massNumber of molelcules
Total (without water)26,3612
Polymers26,3612
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-26 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.000, 62.620, 63.660
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 ALPHA-CATENIN


Mass: 22694.391 Da / Num. of mol.: 1 / Fragment: DIMERIZATION AND BETA-CATENIN BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P26231
#2: Protein/peptide BETA-CATENIN


Mass: 3666.949 Da / Num. of mol.: 1 / Fragment: ALPHA-CATENIN BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 monomethylether, HEPES, urea, ethanol, Dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
2200 mMHEPES1reservoir
325 %mPEG20001reservoir
4240 mMurea1reservoir
53 %ethanol1reservoir
610 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9252
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9252 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 37629 / Num. obs: 36760 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.212 / Num. unique all: 1759 / % possible all: 92.3
Reflection shell
*PLUS
% possible obs: 92.3 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 309534.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2863 7.8 %RANDOM
Rwork0.2 ---
obs0.2 36760 96.9 %-
all-36760 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.93 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.87 Å20 Å20 Å2
2--0.76 Å20 Å2
3---6.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 252 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 297 9.2 %
Rwork0.24 2945 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 33897
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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