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- PDB-1t08: Crystal structure of beta-catenin/ICAT helical domain/unphosphory... -

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Basic information

Entry
Database: PDB / ID: 1t08
TitleCrystal structure of beta-catenin/ICAT helical domain/unphosphorylated APC R3
Components
  • Adenomatous polyposis coli protein
  • Beta-catenin
  • Beta-catenin-interacting protein 1
Keywordscell adhesion/cell cycle / beta-catenin / Wnt signal / APC / 20mer repeat / Wnt signaling / cell adhesion-cell cycle COMPLEX
Function / homology
Function and homology information


regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / APC truncation mutants are not K63 polyubiquitinated / negative regulation of mesenchymal cell proliferation / armadillo repeat domain binding / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation ...regulation of vascular permeability involved in acute inflammatory response / negative regulation of transcription initiation by RNA polymerase II / APC truncation mutants are not K63 polyubiquitinated / negative regulation of mesenchymal cell proliferation / armadillo repeat domain binding / 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 / CDH11 homotypic and heterotypic interactions / 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 CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / 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 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / negative regulation of cell cycle G1/S phase transition / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / beta-catenin-TCF complex / gamma-catenin binding / acinar cell differentiation / dorsal root ganglion development / endodermal cell fate commitment / synaptic vesicle clustering / neuron fate determination / proximal/distal pattern formation / Formation of the nephric duct / endothelial tube morphogenesis / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of microtubule-based movement / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of attachment of spindle microtubules to kinetochore / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / lung epithelial cell differentiation / positive regulation of pseudopodium assembly / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / hair cell differentiation / ectoderm development / embryonic foregut morphogenesis / detection of muscle stretch / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of protein localization to centrosome / positive regulation of myoblast proliferation / alpha-catenin binding / histone methyltransferase binding / regulation of calcium ion import / regulation of epithelial to mesenchymal transition / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / bicellular tight junction assembly / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / pattern specification process / positive regulation of epithelial cell proliferation involved in prostate gland development / cranial skeletal system development / cell-cell adhesion mediated by cadherin / negative regulation of microtubule depolymerization / male genitalia development / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm
Similarity search - Function
Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein ICAT / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family ...Beta-catenin-interacting ICAT / Beta-catenin-interacting ICAT domain / Beta-catenin-interacting ICAT superfamily / Beta-catenin-interacting protein ICAT / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / 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
Adenomatous polyposis coli protein / Catenin beta-1 / Beta-catenin-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHa, N.-C. / Tonozuka, T. / Stamos, J.L. / Weis, W.I.
CitationJournal: Mol.Cell / Year: 2004
Title: Mechanism of phosphorylation-dependent binding of APC to beta-catenin and its role in beta-catenin degradation
Authors: Ha, N.-C. / Tonozuka, T. / Stamos, J.L. / Choi, H.J. / Weis, W.I.
History
DepositionApr 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
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: Beta-catenin-interacting protein 1
C: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)63,4563
Polymers63,4563
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.472, 96.712, 86.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Beta-catenin / cadherin-associated protein / PRO2286


Mass: 56583.680 Da / Num. of mol.: 1 / Fragment: armadillo repeat (RESIDUES 146-664)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1,CTNNB / Plasmid: pPROEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35222
#2: Protein/peptide Beta-catenin-interacting protein 1 / beta-catenin-interacting protein ICAT / Inhibitor of beta-catenin and Tcf-4


Mass: 5239.055 Da / Num. of mol.: 1 / Fragment: helical domain (RESIDUES 8-53)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNBIP1,ICAT / Plasmid: pPROEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NSA3
#3: Protein/peptide Adenomatous polyposis coli protein / APC / APC protein


Mass: 1633.688 Da / Num. of mol.: 1 / Fragment: repeat 3 (RESIDUES 1484-1498)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APC,DP2.5 / Plasmid: pGEXTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25054
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.07 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 6.5
Details: PEG3400, Potassium phosphate, pH 6.5, EVAPORATION, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorSINGLE WAVELENGTHMx-ray1
2mirrorSINGLE WAVELENGTHMx-ray1
3mirrorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 47853 / Num. obs: 47853 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.67 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.16 / Num. unique all: 4230 / Rsym value: 0.296 / % possible all: 90.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1E

1m1e


Resolution: 2.1→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 465671.86 / 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
Rfree0.241 2280 5 %RANDOM
Rwork0.204 ---
all0.215 47853 --
obs0.215 45577 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2511 Å2 / ksol: 0.365862 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--3.93 Å20 Å2
3----2.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 327 4697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.52.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 334 4.7 %
Rwork0.293 6848 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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