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- PDB-1m1e: Beta-catenin armadillo repeat domain bound to ICAT -

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Basic information

Entry
Database: PDB / ID: 1m1e
TitleBeta-catenin armadillo repeat domain bound to ICAT
Components
  • Beta-catenin
  • ICAT
KeywordsSTRUCTURAL PROTEIN / Cell adhesion / Cytoskeleton / Armadillo repeats / transciption factor
Function / homology
Function and homology information


regulation of vascular permeability involved in acute inflammatory response / 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 / negative regulation of mesenchymal cell proliferation ...regulation of vascular permeability involved in acute inflammatory response / 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 / negative regulation of mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / 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 / armadillo repeat domain binding / 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 / positive regulation of fibroblast growth factor receptor signaling pathway / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / 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
Similarity search - Function
Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein ICAT / Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant ...Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein ICAT / 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 / Arc Repressor Mutant, subunit A / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Beta-catenin-interacting protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDaniels, D.L. / Weis, W.I.
CitationJournal: Mol.Cell / Year: 2002
Title: ICAT inhibits Beta-catenin binding to Tcf/Lef-family transcription factors and the general coactivator p300 using independent structural modules.
Authors: Daniels, D.L. / Weis, W.I.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-catenin
B: ICAT


Theoretical massNumber of molelcules
Total (without water)68,0252
Polymers68,0252
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-10 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.750, 97.320, 86.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-catenin


Mass: 58844.117 Da / Num. of mol.: 1 / Fragment: Armadillo Repeat Region (RESIDUES 134-671)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): Topp3 / References: UniProt: Q02248
#2: Protein ICAT


Mass: 9181.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NSA3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, MPD, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMMES1reservoirpH6.5
35 mMdithiothreitol1reservoir
41-2 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2001
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 55512 / Num. obs: 47814 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.25 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
COMOphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I7W

1i7w


Resolution: 2.1→43.56 Å / Rfactor Rfree error: 0.005 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2415 5.1 %RANDOM
Rwork0.202 ---
obs0.202 47814 97.4 %-
all-47814 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0775 Å2 / ksol: 0.34978 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2--6.75 Å20 Å2
3----9.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 310 4708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 389 4.9 %
Rwork0.212 7473 -
obs-389 97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.202 / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.246 / Rfactor Rwork: 0.212

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