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- PDB-1jdh: CRYSTAL STRUCTURE OF BETA-CATENIN AND HTCF-4 -

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Basic information

Entry
Database: PDB / ID: 1jdh
TitleCRYSTAL STRUCTURE OF BETA-CATENIN AND HTCF-4
Components
  • BETA-CATENINCatenin beta-1
  • hTcf-4
KeywordsTRANSCRIPTION / BETA-CATENIN / TCF4 / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


catenin-TCF7L2 complex / regulation of hormone metabolic process / negative regulation of type B pancreatic cell apoptotic process / Signaling by TCF7L2 mutants / Repression of WNT target genes / maintenance of DNA repeat elements / myoblast fate commitment / armadillo repeat domain binding / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function ...catenin-TCF7L2 complex / regulation of hormone metabolic process / negative regulation of type B pancreatic cell apoptotic process / Signaling by TCF7L2 mutants / Repression of WNT target genes / maintenance of DNA repeat elements / myoblast fate commitment / 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 / 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 / embryonic axis specification / endodermal cell fate commitment / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / gamma-catenin binding / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / sympathetic ganglion development / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / positive regulation of odontoblast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / 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 / male genitalia development / negative regulation of oligodendrocyte differentiation / fascia adherens / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / embryonic brain development / Formation of definitive endoderm / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / oocyte development / beta-catenin destruction complex / lung-associated mesenchyme development / Formation of axial mesoderm / negative regulation of protein sumoylation / adherens junction assembly
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGraham, T.A. / Ferkey, D.M. / Mao, F. / Kimelman, D. / Xu, W.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Tcf4 can specifically recognize beta-catenin using alternative conformations.
Authors: Graham, T.A. / Ferkey, D.M. / Mao, F. / Kimelman, D. / Xu, W.
History
DepositionJun 13, 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 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
B: hTcf-4


Theoretical massNumber of molelcules
Total (without water)61,8312
Polymers61,8312
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-12 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.770, 76.033, 159.129
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 / Catenin beta-1


Mass: 57699.902 Da / Num. of mol.: 1 / Fragment: Residues 135-663
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/peptide hTcf-4


Mass: 4131.336 Da / Num. of mol.: 1 / Fragment: Residues 12-49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQB0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal grow
*PLUS
pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
210 mMHEPES1droppH7.5
325 mM1dropNaCl
45 mMdithiothreitol1drop
52.5 %(w/v)PEG80001reservoir
644 mMphosphate-citrate1reservoirpH4.2
710 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1.063
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 47949 / % possible obs: 98.8 % / Redundancy: 9.98 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.76 / Net I/σ(I): 23.9
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.306

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 727211.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3812 9.7 %RANDOM
Rwork0.203 ---
obs0.203 39403 81.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.16 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--4.49 Å20 Å2
3----5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 0 393 4418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 160 5 %
Rwork0.221 3019 -
obs--40 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 36861 / σ(F): 2 / Num. reflection Rfree: 3719 / % reflection Rfree: 9.7 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 5 % / Rfactor Rwork: 0.221

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