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- PDB-1jpw: Crystal Structure of a Human Tcf-4 / beta-Catenin Complex -

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Basic information

Entry
Database: PDB / ID: 1jpw
TitleCrystal Structure of a Human Tcf-4 / beta-Catenin Complex
Components
  • BETA-CATENIN
  • transcription factor 7-like 2
KeywordsCELL ADHESION / beta-catenin / tcf / tcf4 / colon cancer / armadillo repeat / transcription factor
Function / homology
Function and homology information


catenin-TCF7L2 complex / negative regulation of type B pancreatic cell apoptotic process / regulation of hormone metabolic process / Signaling by TCF7L2 mutants / Repression of WNT target genes / armadillo repeat domain binding / myoblast fate commitment / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis ...catenin-TCF7L2 complex / negative regulation of type B pancreatic cell apoptotic process / regulation of hormone metabolic process / Signaling by TCF7L2 mutants / Repression of WNT target genes / armadillo repeat domain binding / myoblast fate commitment / 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 / maintenance of DNA repeat elements / 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 / 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 / positive regulation of fibroblast growth factor receptor signaling pathway / 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 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 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 / negative regulation of androgen receptor signaling pathway / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / cranial skeletal system development / cell-cell adhesion mediated by cadherin / male genitalia development / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / catenin complex / embryonic brain development / beta-catenin destruction complex / lung-associated mesenchyme development
Similarity search - Function
c-clamp / 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. ...c-clamp / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Transcription factor 7-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPoy, F. / Lepourcelet, M. / Shivdasani, R.A. / Eck, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of a human Tcf4-beta-catenin complex.
Authors: Poy, F. / Lepourcelet, M. / Shivdasani, R.A. / Eck, M.J.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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 / 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: BETA-CATENIN
D: transcription factor 7-like 2
B: BETA-CATENIN
E: transcription factor 7-like 2
C: BETA-CATENIN
F: transcription factor 7-like 2


Theoretical massNumber of molelcules
Total (without water)192,5126
Polymers192,5126
Non-polymers00
Water15,277848
1
A: BETA-CATENIN
D: transcription factor 7-like 2


Theoretical massNumber of molelcules
Total (without water)64,1712
Polymers64,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-9 kcal/mol
Surface area22240 Å2
MethodPISA
2
B: BETA-CATENIN
E: transcription factor 7-like 2


Theoretical massNumber of molelcules
Total (without water)64,1712
Polymers64,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-11 kcal/mol
Surface area22380 Å2
MethodPISA
3
C: BETA-CATENIN
F: transcription factor 7-like 2


Theoretical massNumber of molelcules
Total (without water)64,1712
Polymers64,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)376.530, 92.650, 49.250
Angle α, β, γ (deg.)90.00, 95.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-882-

HOH

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Components

#1: Protein BETA-CATENIN


Mass: 58990.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35222
#2: Protein/peptide transcription factor 7-like 2 / Tcf4


Mass: 5180.256 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NQB0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 400, MES, ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 22K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMHEPES1droppH7.5
2200 mM1dropNaCl
35 mMdithiothreitol1drop
47.5 mg/mlprotein1drop
514 %(w/v)PEG40001reservoir
6100 mMMES1reservoirpH5.5
7100 mMammonium sulfate1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 165 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2000 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / % possible obs: 88.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.123

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCT

2bct


Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3898 2249 -random
Rwork0.3045 ---
all0.3045 58414 --
obs0.3045 44044 86 %-
Solvent computationBsol: 82.2046 Å2 / ksol: 0.325126 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.684 Å20 Å20.328 Å2
2--4.105 Å20 Å2
3---0.579 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11919 0 0 848 12767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007573
X-RAY DIFFRACTIONc_angle_deg1.34
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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