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- PDB-2gl7: Crystal Structure of a beta-catenin/BCL9/Tcf4 complex -

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Basic information

Entry
Database: PDB / ID: 2gl7
TitleCrystal Structure of a beta-catenin/BCL9/Tcf4 complex
Components
  • B-cell lymphoma 9 protein
  • Beta-catenin
  • Transcription factor 7-like 2
KeywordsTRANSCRIPTION / PROTEIN COMPLEX / ARMADILLO REPEAT
Function / homology
Function and homology information


catenin-TCF7L2 complex / myotube differentiation involved in skeletal muscle regeneration / negative regulation of type B pancreatic cell apoptotic process / Signaling by TCF7L2 mutants / regulation of hormone metabolic process / Repression of WNT target genes / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / armadillo repeat domain binding / myoblast fate commitment / positive regulation of heparan sulfate proteoglycan biosynthetic process ...catenin-TCF7L2 complex / myotube differentiation involved in skeletal muscle regeneration / negative regulation of type B pancreatic cell apoptotic process / Signaling by TCF7L2 mutants / regulation of hormone metabolic process / Repression of WNT target genes / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / 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 / maintenance of DNA repeat elements / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / 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 / regulation of secondary heart field cardioblast proliferation / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / embryonic skeletal limb joint morphogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / acinar cell differentiation / embryonic axis specification / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / neuron fate determination / beta-catenin-TCF complex / Specification of the neural plate border / synaptic vesicle clustering / endodermal cell fate commitment / Formation of the nephric duct / proximal/distal pattern formation / endothelial tube morphogenesis / dorsal root ganglion development / gamma-catenin binding / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal/ventral axis specification / sympathetic ganglion development / lung epithelial cell differentiation / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / layer formation in cerebral cortex / positive regulation of skeletal muscle tissue development / mesenchymal to epithelial transition / hindbrain development / fungiform papilla formation / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / positive regulation of myoblast proliferation / ectoderm development / embryonic foregut morphogenesis / detection of muscle stretch / mesenchymal cell proliferation involved in lung development / positive regulation of odontoblast differentiation / hair cell differentiation / smooth muscle cell differentiation / alpha-catenin binding / histone methyltransferase binding / cellular response to indole-3-methanol / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / epithelial cell proliferation involved in prostate gland development / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of androgen receptor signaling pathway / male genitalia development / flotillin complex / cranial skeletal system development / Formation of definitive endoderm / cell-cell adhesion mediated by cadherin / lung-associated mesenchyme development / regulation of smooth muscle cell proliferation / midbrain dopaminergic neuron differentiation / cis-Golgi network
Similarity search - Function
c-clamp / CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / Beta-catenin / Catenin binding domain superfamily / HMG (high mobility group) box ...c-clamp / CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / 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 / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
B-cell CLL/lymphoma 9 protein / Catenin beta-1 / Transcription factor 7-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSampietro, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal Structure of a beta-Catenin/BCL9/Tcf4 Complex.
Authors: Sampietro, J. / Dahlberg, C.L. / Cho, U.S. / Hinds, T.R. / Kimelman, D. / Xu, W.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-catenin
B: Transcription factor 7-like 2
C: B-cell lymphoma 9 protein
D: Beta-catenin
E: Transcription factor 7-like 2
F: B-cell lymphoma 9 protein


Theoretical massNumber of molelcules
Total (without water)142,3186
Polymers142,3186
Non-polymers00
Water2,306128
1
A: Beta-catenin
B: Transcription factor 7-like 2
C: B-cell lymphoma 9 protein


Theoretical massNumber of molelcules
Total (without water)71,1593
Polymers71,1593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-26 kcal/mol
Surface area23960 Å2
MethodPISA
2
D: Beta-catenin
E: Transcription factor 7-like 2
F: B-cell lymphoma 9 protein


Theoretical massNumber of molelcules
Total (without water)71,1593
Polymers71,1593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.764, 119.441, 130.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-42-

HOH

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Components

#1: Protein Beta-catenin


Mass: 60240.664 Da / Num. of mol.: 2 / Fragment: Residues 138-686 / Mutation: Y142E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB / Plasmid: pET-28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: P35222
#2: Protein Transcription factor 7-like 2 / HMG box transcription factor 4 / T- cell-specific transcription factor 4 / TCF-4 / hTCF-4


Mass: 5632.825 Da / Num. of mol.: 2 / Fragment: Residues 1-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCF7L2, TCF4 / Plasmid: pET-28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star / References: UniProt: Q9NQB0
#3: Protein/peptide B-cell lymphoma 9 protein / Bcl-9 / Legless homolog


Mass: 5285.731 Da / Num. of mol.: 2 / Fragment: Residues 347-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL9 / Plasmid: pET-28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: O00512
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEG 3350, 125mM sodium thiocyanate, 5% Glycerol, 10mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2005
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 57945 / Num. obs: 55482 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 75.3

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data reduction
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / SU B: 9.997 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26699 2359 5 %RANDOM
Rwork0.22082 ---
obs0.2231 44428 99.12 %-
all-46787 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1-6.91 Å20 Å20 Å2
2---3.03 Å20 Å2
3----3.88 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8301 0 0 128 8429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218407
X-RAY DIFFRACTIONr_bond_other_d0.0020.027980
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.96511426
X-RAY DIFFRACTIONr_angle_other_deg0.828318421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.66351106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021513
X-RAY DIFFRACTIONr_nbd_refined0.1780.22056
X-RAY DIFFRACTIONr_nbd_other0.1950.28755
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.25070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.371.55538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71628843
X-RAY DIFFRACTIONr_scbond_it1.04232869
X-RAY DIFFRACTIONr_scangle_it1.8954.52583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 136
Rwork0.325 2949
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1764-0.0824-0.48030.519-0.39221.87130.0721-0.01250.01580.07710.035-0.0701-0.10430.0057-0.1070.0906-0.0276-0.04340.2155-0.00660.24115.91313.50443.671
20.52780.26530.3632-0.297-1.777612.2492-0.0034-0.0960.0166-0.0083-0.1695-0.01670.56770.00040.17290.2590.0002-0.00030.2586-0.00020.258814.43812.93536.128
322.421820.8637-9.87238.2909-8.025517.86920.21720.68660.2417-1.3142-0.0959-0.556-0.88830.6496-0.12130.2589-0.0003-0.00030.259-0.00020.259226.7216.384-17.185
40.86120.19231.50130.60220.3723.59550.0235-0.18530.10860.0263-0.13210.0671-0.0309-0.31950.10870.0111-0.01660.05340.2147-0.04870.262540.095-16.80715.247
50.72990.06770.408-0.83970.341926.1891-0.2601-0.09870.0281-0.0701-0.12130.0651-1.82620.16690.38140.2599-0.00030.00110.25890.00010.259241.786-16.4617.502
667.149121.8557-8.401819.4752-7.627232.4421-0.01240.5006-0.0651-0.01630.25010.6318-0.2945-0.483-0.23770.25920.0001-0.00040.2594-0.00020.259122.082-13.279-45.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA142 - 5496 - 413
2X-RAY DIFFRACTION1AA560 - 663424 - 527
3X-RAY DIFFRACTION2BB12 - 2812 - 28
4X-RAY DIFFRACTION2BB40 - 5040 - 50
5X-RAY DIFFRACTION3CC352 - 3746 - 28
6X-RAY DIFFRACTION4DD147 - 54911 - 413
7X-RAY DIFFRACTION4DD560 - 662424 - 526
8X-RAY DIFFRACTION5EE12 - 2812 - 28
9X-RAY DIFFRACTION5EE40 - 5040 - 50
10X-RAY DIFFRACTION6FF355 - 3719 - 25

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