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- PDB-1luj: Crystal Structure of the Beta-catenin/ICAT Complex -

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Basic information

Entry
Database: PDB / ID: 1luj
TitleCrystal Structure of the Beta-catenin/ICAT Complex
Components
  • Beta-catenin-interacting protein 1
  • Catenin beta-1
KeywordsSTRUCTURAL PROTEIN / Beta-catenin / ICAT / Wnt pathway / inhibitor
Function / homology
Function and homology information


regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / negative regulation of mesenchymal cell proliferation / armadillo repeat domain binding / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development ...regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / negative regulation of mesenchymal cell proliferation / armadillo repeat domain binding / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / 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 / 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 / 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 / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / RUNX3 regulates WNT signaling / regulation of centriole-centriole cohesion / Regulation of CDH11 function / regulation of centromeric sister chromatid cohesion / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / 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 / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / 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 / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of skeletal muscle tissue development / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / flotillin complex / establishment of blood-brain barrier / Germ layer formation at gastrulation / negative regulation of oligodendrocyte differentiation / male genitalia development / fascia adherens / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / embryonic brain development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / adherens junction assembly / beta-catenin destruction complex / oocyte development / Formation of axial mesoderm / lung-associated mesenchyme development / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / positive regulation of monocyte differentiation / embryonic heart tube development
Similarity search - Function
Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein 1 / Beta-catenin-interacting protein ICAT / Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo ...Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein 1 / 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 speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGraham, T.A. / Clements, W.K. / Kimelman, D. / Xu, W.
CitationJournal: Mol.Cell / Year: 2002
Title: The crystal structure of the beta-catenin/ICAT complex reveals the inhibitory mechanism of ICAT.
Authors: Graham, T.A. / Clements, W.K. / Kimelman, D. / Xu, W.
History
DepositionMay 22, 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 1.3Mar 16, 2016Group: Source and taxonomy
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Beta-catenin-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)64,4962
Polymers64,4962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-8 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.174, 98.504, 86.486
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 Catenin beta-1 / Beta-catenin


Mass: 56070.137 Da / Num. of mol.: 1 / Fragment: residues 150-666
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / References: UniProt: P35222
#2: Protein Beta-catenin-interacting protein 1 / Inhibitor of beta-catenin and Tcf-4


Mass: 8425.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo / Gene: Ctnnbip1, Catnbip1, Icat / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JJN6

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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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG800, magnesium chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
24 %(w/v)PEG80001reservoir
320 mM1reservoirMgCl2
450 mMTris1reservoirpH8.0
55 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9196 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 16, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23804 / Num. obs: 23804 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.119 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.65 / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 2.51 Å / Lowest resolution: 50 Å / Num. measured all: 163681 / Rmerge(I) obs: 0.119
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.65

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.74 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2378 10 %RANDOM
Rwork0.21 ---
all0.215 23804 --
obs0.21 23804 82.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.131 Å2 / ksol: 0.370507 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2--2.67 Å20 Å2
3----5.26 Å2
Refine analyzeLuzzati coordinate error free: 0.36 Å / Luzzati sigma a free: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 0 0 4216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 263 9.9 %
Rwork0.232 2387 -
obs--56.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Num. reflection obs: 23745 / Rfactor all: 0.215 / Rfactor obs: 0.21 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.211 / Highest resolution: 2.51 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.3 / Rfactor Rwork: 0.232

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