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- PDB-3diw: c-terminal beta-catenin bound TIP-1 structure -

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Basic information

Entry
Database: PDB / ID: 3diw
Titlec-terminal beta-catenin bound TIP-1 structure
Components
  • Tax1-binding protein 3
  • decameric peptide form Catenin beta-1
KeywordsSIGNALING PROTEIN/CELL ADHESION / beta-catenin / TIP-1 / Tax-interacting protein-1 / PDZ domain / Nucleus / Wnt signaling pathway / SIGNALING PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic ...positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / Specification of the neural plate border / positive regulation of skeletal muscle tissue development / synaptic vesicle clustering / Formation of the nephric duct / negative regulation of protein localization to cell surface / dorsal root ganglion development / endothelial tube morphogenesis / hindbrain development / mesenchymal to epithelial transition / cranial skeletal system development / sympathetic ganglion development / presynaptic active zone cytoplasmic component / regulation of protein localization to cell surface / fascia adherens / mesenchymal stem cell differentiation / detection of muscle stretch / positive regulation of odontoblast differentiation / alpha-catenin binding / cellular response to indole-3-methanol / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / histone methyltransferase binding / hair cell differentiation / apicolateral plasma membrane / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / neuron projection extension / cell-cell adhesion mediated by cadherin / flotillin complex / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / beta-catenin destruction complex / Formation of axial mesoderm / embryonic brain development / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / midbrain dopaminergic neuron differentiation / catenin complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of blood vessel branching / protein localization to cell surface / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / I-SMAD binding / Regulation of CDH1 Function / Wnt signalosome / Adherens junctions interactions / regulation of Cdc42 protein signal transduction / adherens junction assembly / positive regulation of neuroblast proliferation / Cardiogenesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / stem cell population maintenance / Myogenesis / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / hypothalamus development / Formation of paraxial mesoderm / regulation of synapse assembly / Somitogenesis / microvillus membrane / SMAD binding / outflow tract morphogenesis / canonical Wnt signaling pathway / Regulation of MITF-M-dependent genes involved in pigmentation / Transcriptional Regulation by VENTX / negative regulation of Wnt signaling pathway / epithelial to mesenchymal transition / regulation of protein ubiquitination / Rho protein signal transduction / regulation of angiogenesis / lateral plasma membrane / regulation of neurogenesis / bicellular tight junction / positive regulation of epithelial to mesenchymal transition / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / phosphatase binding / postsynaptic density, intracellular component
Similarity search - Function
Tax1-binding protein 3 / Beta-catenin / : / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / Pdz3 Domain / PDZ domain ...Tax1-binding protein 3 / Beta-catenin / : / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / Armadillo-type fold / Roll / Mainly Beta
Similarity search - Domain/homology
Catenin beta-1 / Tax1-binding protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShen, Y.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Basis of beta-Catenin Recognition by Tax-interacting Protein-1
Authors: Zhang, J. / Yan, X. / Shi, C. / Yang, X. / Guo, Y. / Tian, C. / Long, J. / Shen, Y.
History
DepositionJun 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Derived calculations
Revision 1.3Nov 1, 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: Tax1-binding protein 3
B: Tax1-binding protein 3
C: decameric peptide form Catenin beta-1
D: decameric peptide form Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)29,9244
Polymers29,9244
Non-polymers00
Water3,351186
1
A: Tax1-binding protein 3
C: decameric peptide form Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)14,9622
Polymers14,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-5 kcal/mol
Surface area6820 Å2
MethodPISA
2
B: Tax1-binding protein 3
D: decameric peptide form Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)14,9622
Polymers14,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.098, 93.571, 107.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tax1-binding protein 3 / Tax interaction protein 1 / TIP-1


Mass: 13739.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DBG9
#2: Protein/peptide decameric peptide form Catenin beta-1 / Beta-catenin


Mass: 1222.303 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 772-781 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P35222
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3.0M sodium formate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2008
RadiationProtocol: 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: 16802 / Num. obs: 16450 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1357 / Rsym value: 0.357 / % possible all: 84.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BE9

1be9


Resolution: 2.1→29.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 167362.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1569 10 %RANDOM
Rwork0.221 ---
obs0.221 15683 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3317 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2--1.48 Å20 Å2
3---1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 0 186 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 196 9.2 %
Rwork0.264 1937 -
obs--78.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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