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- PDB-3ouw: Structure of beta-catenin with Lef-1 -

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Basic information

Entry
Database: PDB / ID: 3ouw
TitleStructure of beta-catenin with Lef-1
Components
  • Catenin beta-1
  • Lymphoid enhancer-binding factor 1
KeywordsPROTEIN BINDING / Wnt/beta-catenin signaling pathway / TCF / Lef / transcription factors / phosphorylation
Function / homology
Function and homology information


Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling ...Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / 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 interleukin-4 production / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of granulocyte differentiation / Beta-catenin phosphorylation cascade / T cell receptor V(D)J recombination / Apoptotic cleavage of cell adhesion proteins / negative regulation of interleukin-5 production / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of interleukin-13 production / hair cycle process / morphogenesis of embryonic epithelium / positive regulation of epithelial cell differentiation / TCF dependent signaling in response to WNT / neutrophil differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / trachea morphogenesis / negative regulation of apoptotic process in bone marrow cell / T-helper 1 cell differentiation / mesenchyme development / endoderm formation / Formation of the beta-catenin:TCF transactivating complex / armadillo repeat domain binding / VEGFR2 mediated vascular permeability / negative regulation of striated muscle tissue development / 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 / mesenchymal stem cell differentiation / apoptotic process involved in blood vessel morphogenesis / beta-catenin-ICAT complex / metanephros morphogenesis / formation of radial glial scaffolds / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / positive regulation of cell proliferation in bone marrow / neural plate development / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / 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 / negative regulation of mitotic cell cycle, embryonic / regulation of epithelial cell differentiation / Ca2+ pathway / Schwann cell proliferation / apoptotic process involved in morphogenesis / central nervous system vasculogenesis / odontoblast differentiation / animal organ development / regulation of centriole-centriole cohesion / Adherens junctions interactions / RHO GTPases activate IQGAPs / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / ventricular compact myocardium morphogenesis / embryonic axis specification / cell development / secondary palate development / endodermal cell fate commitment / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / mesenchymal cell proliferation involved in lung development / beta-catenin-TCF complex / dorsal root ganglion development / positive regulation of gamma-delta T cell differentiation / gamma-catenin binding / synaptic vesicle clustering / acinar cell differentiation / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / dorsal/ventral axis specification / positive regulation of endothelial cell differentiation / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / fungiform papilla formation
Similarity search - Function
CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / Beta-catenin / Catenin binding domain superfamily / HMG (high mobility group) box / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / HMG boxes A and B DNA-binding domains profile. / high mobility group ...CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / Beta-catenin / Catenin binding domain superfamily / HMG (high mobility group) box / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Lymphoid enhancer-binding factor 1 / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsWeis, W.I. / Sun, J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Biochemical and structural characterization of beta-catenin interactions with nonphosphorylated and CK2-phosphorylated Lef-1.
Authors: Sun, J. / Weis, W.I.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Dec 9, 2015Group: Other
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Lymphoid enhancer-binding factor 1


Theoretical massNumber of molelcules
Total (without water)65,8212
Polymers65,8212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-12 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.93, 116.93, 214.15
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 58988.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctnnb1, Catnb / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#2: Protein Lymphoid enhancer-binding factor 1 / LEF-1


Mass: 6832.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lef1, Lef-1 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / References: UniProt: P27782
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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: well solution: 4.2% PEG 4000, 100 mM sodium citrate. protein solution: 100 uM beta-cat-arm, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97922 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.9→103 Å / Num. obs: 15960 / % possible obs: 96.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 13
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.1 / % possible all: 82.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: beta-catenin arm domain from beta-catenin/phosphorylated Lef-1 structure

Resolution: 2.91→44.94 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 630 3.95 %RANDOM
Rwork0.203 ---
obs-15960 95.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.127 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.7144 Å2-0 Å20 Å2
2---16.7144 Å2-0 Å2
3---33.4288 Å2
Refinement stepCycle: LAST / Resolution: 2.91→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 0 0 3963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084018
X-RAY DIFFRACTIONf_angle_d1.1915449
X-RAY DIFFRACTIONf_dihedral_angle_d16.5481486
X-RAY DIFFRACTIONf_chiral_restr0.068668
X-RAY DIFFRACTIONf_plane_restr0.005697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.19960.3287450.30423310X-RAY DIFFRACTION82
3.1996-3.66240.34351090.25084002X-RAY DIFFRACTION99
3.6624-4.61350.22011880.1763971X-RAY DIFFRACTION100
4.6135-44.94460.25232880.17324047X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3934-0.04820.07630.5065-0.16620.066-0.27260.71160.0608-0.28740.1219-0.08860.3735-0.26890.16160.6825-0.40330.09271.29730.20370.37731.548234.1569-44.939
20.95140.1124-0.61820.9345-0.11061.0796-0.01840.14620.1958-0.2016-0.00890.4357-0.04780.0167-0.0045-0.2299-0.02990.23630.03190.0394-0.1238-23.749438.74495.1104
31.6152-0.4833-0.31821.5077-0.29310.2516-0.06450.26390.49160.24850.19780.1581-0.0947-0.1034-0.12590.28430.088-0.02110.31120.14870.5404-28.722233.88579.6978
40.1660.2648-0.0260.4235-0.04870.04390.0670.0076-0.001-0.02840.1006-0.0055-0.0037-0.1162-0.15950.4243-0.07260.04020.5440.26560.86865.70240.7864-27.2546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 157:236)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 237:664)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 11:25)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 48:60)

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