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- PDB-4evt: Crystal Structure of Mouse Catenin beta-59 in 8.3M urea -

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Basic information

Entry
Database: PDB / ID: 4evt
TitleCrystal Structure of Mouse Catenin beta-59 in 8.3M urea
ComponentsCatenin beta-1
KeywordsCELL ADHESION / mouse beta catenin / urea
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 / 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 ...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 / 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 / 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 / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / 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 / animal organ development / VEGFR2 mediated vascular permeability / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of epithelial cell differentiation / regulation of centriole-centriole cohesion / Adherens junctions interactions / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / morphogenesis of embryonic epithelium / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / acinar cell differentiation / dorsal root ganglion development / endodermal cell fate commitment / synaptic vesicle clustering / neuron fate determination / proximal/distal pattern formation / endothelial tube morphogenesis / ventricular compact myocardium morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / ectoderm development / embryonic foregut morphogenesis / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of myoblast proliferation / alpha-catenin binding / histone methyltransferase binding / mesenchymal cell proliferation / regulation of calcium ion import / regulation of epithelial to mesenchymal transition / cell projection membrane / positive regulation of homotypic cell-cell adhesion / regulation of osteoclast differentiation / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / Myogenesis
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
UREA / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.339 Å
AuthorsWang, C. / Zhang, G.Y.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Mouse Catenin beta-59 in 8.3M urea
Authors: Wang, C. / Zhang, G.Y.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,20757
Polymers58,8441
Non-polymers3,36356
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.748, 102.606, 187.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-701-

URE

21A-701-

URE

31A-805-

HOH

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Components

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


Mass: 58844.117 Da / Num. of mol.: 1 / Fragment: unp residues 134-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q02248
#2: Chemical...
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6~3.2 M Urea, 200mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.339→50 Å / Num. obs: 29366 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rsym value: 0.07 / Net I/σ(I): 27
Reflection shellResolution: 2.35→2.4 Å / Mean I/σ(I) obs: 1.16 / Rsym value: 0.792 / % possible all: 75.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.339→46.995 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1494 5.08 %
Rwork0.1907 --
obs0.1925 29366 99.77 %
all-24882 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.028 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7073 Å20 Å2-0 Å2
2--9.1441 Å20 Å2
3----8.4369 Å2
Refinement stepCycle: LAST / Resolution: 2.339→46.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 223 86 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053919
X-RAY DIFFRACTIONf_angle_d0.9585273
X-RAY DIFFRACTIONf_dihedral_angle_d13.5281413
X-RAY DIFFRACTIONf_chiral_restr0.061627
X-RAY DIFFRACTIONf_plane_restr0.004702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2548-2.32760.28561480.22932462X-RAY DIFFRACTION98
2.3276-2.41080.2811370.2132506X-RAY DIFFRACTION100
2.4108-2.50730.27271310.20592490X-RAY DIFFRACTION100
2.5073-2.62140.22711330.19892527X-RAY DIFFRACTION100
2.6214-2.75960.24731310.20152528X-RAY DIFFRACTION100
2.7596-2.93250.23221180.20072536X-RAY DIFFRACTION100
2.9325-3.15880.2211270.20182533X-RAY DIFFRACTION100
3.1588-3.47660.24051320.20032540X-RAY DIFFRACTION100
3.4766-3.97950.20511310.17282573X-RAY DIFFRACTION100
3.9795-5.01280.20621510.16512576X-RAY DIFFRACTION100
5.0128-47.00560.2151550.19822668X-RAY DIFFRACTION100

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