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- PDB-3tx7: Crystal structure of LRH-1/beta-catenin complex -

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Basic information

Entry
Database: PDB / ID: 3tx7
TitleCrystal structure of LRH-1/beta-catenin complex
Components
  • Catenin beta-1
  • Nuclear receptor subfamily 5 group A member 2
KeywordsPROTEIN BINDING / LRH-1 / beta-catenin / Armadillo repeat / Nuclear Receptor Ligand Binding Domain
Function / homology
Function and homology information


zygotic genome activation / positive regulation of tendon cell differentiation / inner cell mass cell differentiation / primary ovarian follicle growth / morula formation / Regulation of gene expression in early pancreatic precursor cells / positive regulation of glucocorticoid biosynthetic process / positive regulation of T cell anergy / positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development ...zygotic genome activation / positive regulation of tendon cell differentiation / inner cell mass cell differentiation / primary ovarian follicle growth / morula formation / Regulation of gene expression in early pancreatic precursor cells / positive regulation of glucocorticoid biosynthetic process / positive regulation of T cell anergy / 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 / tissue development / Sertoli cell development / synaptic vesicle clustering / Formation of the nephric duct / exocrine pancreas development / positive regulation of stem cell differentiation / dorsal root ganglion development / endothelial tube morphogenesis / hindbrain development / embryonic cleavage / 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 / homeostatic process / 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 / bile acid metabolic process / 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 / somatic stem cell population maintenance / Apoptotic cleavage of cell adhesion proteins / embryo development ending in birth or egg hatching / midbrain dopaminergic neuron differentiation / catenin complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / negative regulation of chondrocyte differentiation / positive regulation of blood vessel branching / protein localization to cell surface / cartilage development / 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 / hypothalamus development / Formation of paraxial mesoderm / regulation of synapse assembly / Somitogenesis / microvillus membrane
Similarity search - Function
Nuclear hormone receptor family 5 / Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Retinoid X Receptor / Retinoid X Receptor ...Nuclear hormone receptor family 5 / Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-P6L / Nuclear receptor subfamily 5 group A member 2 / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsYumoto, F. / Fletterick, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of coactivation of liver receptor homolog-1 by beta-catenin.
Authors: Yumoto, F. / Nguyen, P. / Sablin, E.P. / Baxter, J.D. / Webb, P. / Fletterick, R.J.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catenin beta-1
B: Nuclear receptor subfamily 5 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2723
Polymers97,5252
Non-polymers7471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-21 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.824, 151.602, 76.131
Angle α, β, γ (deg.)90.00, 96.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Catenin beta-1 / Beta-catenin


Mass: 57517.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286 / Plasmid: pCDF-2 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P35222
#2: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 40007.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Plasmid: pET32 Xa-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: O00482
#3: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mM Tris-HCl, 40% PEG200, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2008
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.75→49.457 Å / Num. all: 28975 / Num. obs: 28946 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.19
Reflection shellResolution: 2.75→2.8 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASER(ccp4)phasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2Z6H, 1YOK

2z6h

1yok


Resolution: 2.76→47.018 Å / SU ML: 0.71 / σ(F): 1.37 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1467 5.08 %
Rwork0.1988 --
obs0.2012 28882 99.76 %
all-27523 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.993 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6533 Å20 Å24.2748 Å2
2--10.8845 Å20 Å2
3----5.2312 Å2
Refinement stepCycle: LAST / Resolution: 2.76→47.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 51 0 5644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085726
X-RAY DIFFRACTIONf_angle_d1.1557748
X-RAY DIFFRACTIONf_dihedral_angle_d18.4212146
X-RAY DIFFRACTIONf_chiral_restr0.074925
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.85350.33081470.24992658X-RAY DIFFRACTION98
2.8535-2.96780.30881580.24092741X-RAY DIFFRACTION100
2.9678-3.10280.3461360.23952756X-RAY DIFFRACTION100
3.1028-3.26640.28851170.24312743X-RAY DIFFRACTION100
3.2664-3.4710.27911540.22542746X-RAY DIFFRACTION100
3.471-3.73890.28591290.2082749X-RAY DIFFRACTION100
3.7389-4.1150.24491610.17392734X-RAY DIFFRACTION100
4.115-4.710.19681500.16062757X-RAY DIFFRACTION100
4.71-5.93250.22151540.20082749X-RAY DIFFRACTION100
5.9325-49.46510.20321610.17482782X-RAY DIFFRACTION100

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