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- PDB-4ev9: Crystal Structure of Mouse Catenin beta-59 in 4.0M urea -

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Basic information

Entry
Database: PDB / ID: 4ev9
TitleCrystal Structure of Mouse Catenin beta-59 in 4.0M urea
ComponentsCatenin beta-1
KeywordsCELL ADHESION / mouse 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 / 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 / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / dorsal/ventral axis specification / sympathetic ganglion development / 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 / cell projection membrane / establishment of blood-brain barrier / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell differentiation involved in prostate gland 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
UREA / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, C. / Zhang, G.Y.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Mouse Catenin beta-59 in 4.0M 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 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)61,36643
Polymers58,8441
Non-polymers2,52242
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.102, 102.618, 187.255
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

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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.: 42 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41 Å / Num. all: 36233 / Num. obs: 36230 / % possible obs: 99.32 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.15 Å / % possible all: 93.2

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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: 2.1→40.996 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1813 5 %
Rwork0.1917 --
obs0.1938 36230 99.32 %
all-36233 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.74 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4309 Å20 Å2-0 Å2
2--7.9779 Å20 Å2
3----3.547 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 168 266 4183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053933
X-RAY DIFFRACTIONf_angle_d0.9015292
X-RAY DIFFRACTIONf_dihedral_angle_d13.7131417
X-RAY DIFFRACTIONf_chiral_restr0.056631
X-RAY DIFFRACTIONf_plane_restr0.004703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.15710.30991290.26992470X-RAY DIFFRACTION94
2.1571-2.22060.25811330.21682566X-RAY DIFFRACTION98
2.2206-2.29220.2171450.1972616X-RAY DIFFRACTION100
2.2922-2.37410.27851470.19892645X-RAY DIFFRACTION100
2.3741-2.46920.23171370.19822630X-RAY DIFFRACTION100
2.4692-2.58150.22381340.1872642X-RAY DIFFRACTION100
2.5815-2.71760.21631290.19642654X-RAY DIFFRACTION100
2.7176-2.88790.23321380.19812669X-RAY DIFFRACTION100
2.8879-3.11080.26141340.19632643X-RAY DIFFRACTION100
3.1108-3.42370.26671410.20222678X-RAY DIFFRACTION100
3.4237-3.91870.20681370.17942684X-RAY DIFFRACTION100
3.9187-4.93590.21061700.1632698X-RAY DIFFRACTION100
4.9359-41.00390.2261390.19832822X-RAY DIFFRACTION100

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