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- PDB-3oux: Structure of beta-catenin with phosphorylated Lef-1 -

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Basic information

Entry
Database: PDB / ID: 3oux
TitleStructure of beta-catenin with phosphorylated 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 / Beta-catenin phosphorylation cascade / positive regulation of granulocyte differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / hair cycle process / positive regulation of epithelial cell differentiation / negative regulation of apoptotic process in bone marrow cell / TCF dependent signaling in response to WNT / armadillo repeat domain binding / neutrophil differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / trachea morphogenesis / negative regulation of striated muscle tissue development / mesenchyme development / endoderm formation / T-helper 1 cell differentiation / Formation of the beta-catenin:TCF transactivating complex / VEGFR2 mediated vascular permeability / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / positive regulation of cell proliferation in bone marrow / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / mesenchymal stem cell differentiation / beta-catenin-ICAT complex / metanephros morphogenesis / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / neural plate development / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / negative regulation of mitotic cell cycle, embryonic / formation of radial glial scaffolds / 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 / Ca2+ pathway / central nervous system vasculogenesis / animal organ development / regulation of epithelial cell differentiation / Schwann cell proliferation / apoptotic process involved in morphogenesis / odontoblast differentiation / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / Degradation of beta-catenin by the destruction complex / RHO GTPases activate IQGAPs / regulation of centromeric sister chromatid cohesion / Adherens junctions interactions / secondary palate development / cell development / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Scrib-APC-beta-catenin complex / regulation of cell-cell adhesion / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / gamma-catenin binding / positive regulation of gamma-delta T cell differentiation / T cell receptor V(D)J recombination / acinar cell differentiation / apoptotic process involved in blood vessel morphogenesis / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation
Similarity search - Function
TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / 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 ...TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / 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 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Few Secondary Structures / Irregular / 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: 2.4 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 1.4Sep 6, 2023Group: 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

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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)66,0092
Polymers66,0092
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-13 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.56, 115.56, 195.93
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-51-

HOH

21A-62-

HOH

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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: 7020.700 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: well solution: 7% PEG 3000, 100 mM sodium citrate. protein solution: 100 micro-M 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: BL9-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4→99.5 Å / Num. obs: 26264 / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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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: PDB ENTRY 1M1E

1m1e


Resolution: 2.4→37.11 Å / SU ML: 0.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1530 5.83 %
Rwork0.199 --
obs-26264 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.936 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5587 Å2-0 Å20 Å2
2---9.5587 Å2-0 Å2
3---19.1175 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 0 97 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084124
X-RAY DIFFRACTIONf_angle_d1.0715604
X-RAY DIFFRACTIONf_dihedral_angle_d14.7861499
X-RAY DIFFRACTIONf_chiral_restr0.07686
X-RAY DIFFRACTIONf_plane_restr0.005725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.30691170.24482203X-RAY DIFFRACTION99
2.4775-2.5660.29521520.21842202X-RAY DIFFRACTION100
2.566-2.66870.29681330.21612206X-RAY DIFFRACTION100
2.6687-2.79010.30381440.21672210X-RAY DIFFRACTION100
2.7901-2.93720.34651390.22262231X-RAY DIFFRACTION100
2.9372-3.12110.3131420.21482235X-RAY DIFFRACTION100
3.1211-3.36190.28271470.22042232X-RAY DIFFRACTION100
3.3619-3.70.28031440.19652244X-RAY DIFFRACTION100
3.7-4.23470.22711160.16822290X-RAY DIFFRACTION100
4.2347-5.33280.22541430.17122296X-RAY DIFFRACTION100
5.3328-37.11490.21091530.18352385X-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)
10.8534-0.7944-0.22181.81810.56590.1775-0.2405-0.23540.01091.34820.34290.0771-0.31270.2872-0.04122.0828-0.20820.17260.56360.0190.251132.36432.144345.7312
20.22280.1645-0.07310.4288-0.04170.2978-0.02940.0389-0.22730.0996-0.0448-0.0147-0.03830.01660.06360.0895-0.00810.01060.0718-0.03940.21538.1135-23.424-5.2077
30.11140.16570.10570.29150.21170.17140.06080.0584-0.07490.03090.1796-0.57930.05670.079-0.23010.15050.0347-0.16280.1601-0.17420.694142.653-22.7032-0.3098
40.1471-0.3810.0361.0315-0.25240.6768-0.0345-0.0197-0.027-0.2626-0.11470.1142-0.88650.17040.14051.3027-0.2708-0.27220.4868-0.04970.483741.17924.207626.8813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 151:236)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 237:665)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 11:42)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 45:60)

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