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- PDB-4ev8: Crystal structure of mouse catenin beta-59 in 2.4M urea. -

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Basic information

Entry
Database: PDB / ID: 4ev8
TitleCrystal structure of mouse catenin beta-59 in 2.4M urea.
ComponentsCatenin beta-1
KeywordsCELL ADHESION / mouse catenin
Function / homology
Function and homology information


metanephros morphogenesis / lung cell differentiation / lung induction / epicardium-derived cardiac vascular smooth muscle cell differentiation / positive regulation of branching involved in lung morphogenesis / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchyme morphogenesis ...metanephros morphogenesis / lung cell differentiation / lung induction / epicardium-derived cardiac vascular smooth muscle cell differentiation / positive regulation of branching involved in lung morphogenesis / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchyme morphogenesis / establishment of blood-retinal barrier / CHD6, CHD7, CHD8, CHD9 subfamily / genitalia morphogenesis / RUNX3 regulates WNT signaling / neural plate development / regulation of secondary heart field cardioblast proliferation / cardiac vascular smooth muscle cell differentiation / glial cell fate determination / Regulation of CDH11 function / oviduct development / central nervous system vasculogenesis / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Schwann cell proliferation / trachea morphogenesis / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / positive regulation of epithelial cell proliferation involved in prostate gland development / Apoptotic cleavage of cell adhesion proteins / ectoderm development / proximal/distal pattern formation / endoderm formation / hair cycle process / embryonic foregut morphogenesis / lens morphogenesis in camera-type eye / Disassembly of the destruction complex and recruitment of AXIN to the membrane / embryonic axis specification / regulation of epithelial cell differentiation / positive regulation of epithelial cell differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / epithelial cell differentiation involved in prostate gland development / establishment of blood-brain barrier / Formation of the beta-catenin:TCF transactivating complex / dorsal/ventral axis specification / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / oocyte development / epithelial tube branching involved in lung morphogenesis / gastrulation with mouth forming second / positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / beta-catenin-ICAT complex / embryonic skeletal limb joint morphogenesis / VEGFR2 mediated vascular permeability / astrocyte-dopaminergic neuron signaling / endodermal cell fate commitment / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / positive regulation of fibroblast growth factor receptor signaling pathway / TCF dependent signaling in response to WNT / Adherens junctions interactions / morphogenesis of embryonic epithelium / layer formation in cerebral cortex / regulation of centriole-centriole cohesion / regulation of centromeric sister chromatid cohesion / mesenchymal cell proliferation involved in lung development / lung-associated mesenchyme development / animal organ development / Deactivation of the beta-catenin transactivating complex / positive regulation of endothelial cell differentiation / trachea formation / embryonic hindlimb morphogenesis / mesenchyme development / Ca2+ pathway / fungiform papilla formation / positive regulation of determination of dorsal identity / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / anterior/posterior axis specification / embryonic forelimb morphogenesis / positive regulation of skeletal muscle tissue development / male genitalia development / synaptic vesicle clustering / Regulation of CDH1 Function / RHO GTPases activate IQGAPs / ventricular compact myocardium morphogenesis / Degradation of CDH1 / endothelial tube morphogenesis / delta-catenin binding / Degradation of beta-catenin by the destruction complex / hindbrain development / dorsal root ganglion development / tissue homeostasis / fascia adherens / mesenchymal to epithelial transition / cranial skeletal system development / sympathetic ganglion development / presynaptic active zone cytoplasmic component
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 / Alpha Horseshoe / Armadillo-like helical / 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: 1.9 Å
AuthorsWang, C. / Zhang, G.Y.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of mouse catenin beta-59 in 2.4M 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 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)59,92519
Polymers58,8441
Non-polymers1,08118
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.185, 102.587, 187.092
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-880-

HOH

41A-894-

HOH

51A-1234-

HOH

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


Mass: 18.015 Da / Num. of mol.: 512 / 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: 53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
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: 1.9→35.5 Å / Num. obs: 48834 / % possible obs: 96.4 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.072 / Net I/σ(I): 26.1
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.7 / % possible all: 90.3

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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
Starting model: PDB ENTRY 3BCT

3bct


Resolution: 1.9→35.47 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 21.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 2391 5.08 %
Rwork0.177 --
obs0.179 47092 96.4 %
all-48834 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.82 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9385 Å20 Å2-0 Å2
2--5.1202 Å20 Å2
3----2.1817 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 72 512 4333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073865
X-RAY DIFFRACTIONf_angle_d1.0285225
X-RAY DIFFRACTIONf_dihedral_angle_d12.6831418
X-RAY DIFFRACTIONf_chiral_restr0.071631
X-RAY DIFFRACTIONf_plane_restr0.006681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9026-1.94140.31621280.24192355X-RAY DIFFRACTION88
1.9414-1.98370.28891280.23762424X-RAY DIFFRACTION91
1.9837-2.02980.25881400.20022475X-RAY DIFFRACTION92
2.0298-2.08060.21171370.17412488X-RAY DIFFRACTION92
2.0806-2.13680.21321190.16752534X-RAY DIFFRACTION93
2.1368-2.19970.22081410.16012537X-RAY DIFFRACTION95
2.1997-2.27070.22521240.17012618X-RAY DIFFRACTION96
2.2707-2.35180.2421450.17382605X-RAY DIFFRACTION97
2.3518-2.44590.21161460.17482666X-RAY DIFFRACTION98
2.4459-2.55720.24111430.17242687X-RAY DIFFRACTION99
2.5572-2.6920.211380.18552700X-RAY DIFFRACTION99
2.692-2.86060.23541570.17972712X-RAY DIFFRACTION100
2.8606-3.08140.22061620.1782697X-RAY DIFFRACTION100
3.0814-3.39120.23911430.17822757X-RAY DIFFRACTION100
3.3912-3.88140.19241300.16582756X-RAY DIFFRACTION100
3.8814-4.88810.1841540.15672788X-RAY DIFFRACTION100
4.8881-35.47580.22361560.1932902X-RAY DIFFRACTION100

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