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- PDB-1g3j: CRYSTAL STRUCTURE OF THE XTCF3-CBD/BETA-CATENIN ARMADILLO REPEAT ... -

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Basic information

Entry
Database: PDB / ID: 1g3j
TitleCRYSTAL STRUCTURE OF THE XTCF3-CBD/BETA-CATENIN ARMADILLO REPEAT COMPLEX
Components
  • BETA-CATENIN ARMADILLO REPEAT REGION
  • TCF3-CBD (CATENIN BINDING DOMAIN)
KeywordsTRANSCRIPTION / Beta-catenin / Tcf-3 / Protein-Protein 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 / endothelial tube morphogenesis / hindbrain development / dorsal root ganglion 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 / regulation of epithelial to mesenchymal transition / alpha-catenin binding / cellular response to indole-3-methanol / histone methyltransferase binding / regulation of calcium ion import / hair cell differentiation / Germ layer formation at gastrulation / apicolateral plasma membrane / 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 / catenin complex / midbrain dopaminergic neuron differentiation / 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 / Adherens junctions interactions / Wnt signalosome / positive regulation of neuroblast proliferation / adherens junction assembly / 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 / regulation of synapse assembly / Formation of paraxial mesoderm / 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 / hypothalamus development / epithelial to mesenchymal transition / regulation of protein ubiquitination / 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 / RHO GTPases activate IQGAPs / positive regulation of telomere maintenance via telomerase / negative regulation of angiogenesis / Transcriptional and post-translational regulation of MITF-M expression and activity
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 / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Transcription factor 7-like 1-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGraham, T.A. / Weaver, C. / Mao, F. / Kimelman, D. / Xu, W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal structure of a beta-catenin/Tcf complex.
Authors: Graham, T.A. / Weaver, C. / Mao, F. / Kimelman, D. / Xu, W.
History
DepositionOct 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 ARMADILLO REPEAT REGION
B: TCF3-CBD (CATENIN BINDING DOMAIN)
C: BETA-CATENIN ARMADILLO REPEAT REGION
D: TCF3-CBD (CATENIN BINDING DOMAIN)


Theoretical massNumber of molelcules
Total (without water)128,9944
Polymers128,9944
Non-polymers00
Water4,738263
1
A: BETA-CATENIN ARMADILLO REPEAT REGION
B: TCF3-CBD (CATENIN BINDING DOMAIN)


Theoretical massNumber of molelcules
Total (without water)64,4972
Polymers64,4972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-11 kcal/mol
Surface area23220 Å2
MethodPISA
2
C: BETA-CATENIN ARMADILLO REPEAT REGION
D: TCF3-CBD (CATENIN BINDING DOMAIN)


Theoretical massNumber of molelcules
Total (without water)64,4972
Polymers64,4972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-13 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.135, 153.249, 188.124
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 BETA-CATENIN ARMADILLO REPEAT REGION


Mass: 58096.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P35222
#2: Protein TCF3-CBD (CATENIN BINDING DOMAIN)


Mass: 6400.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P70062
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.5% PEG-8000, 44mM Phosphate-Citrate, 2mM DTT, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 88997 / Num. obs: 82185 / % possible obs: 92.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.304
Reflection
*PLUS
Num. measured all: 300150
Reflection shell
*PLUS
% possible obs: 94.8 % / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 7442 Random
Rwork0.229 --
all-88997 -
obs-82195 -
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7531 0 0 263 7794
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.04
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / σ(F): 2 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4

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