+Open data
-Basic information
Entry | Database: PDB / ID: 3sl9 | ||||||
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Title | X-ray structure of Beta catenin in complex with Bcl9 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PROTEIN BINDING / Armadillo repeat / components of the Wnt signaling pathway / Beta catenin | ||||||
Function / homology | Function and homology information myotube differentiation involved in skeletal muscle regeneration / 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 ...myotube differentiation involved in skeletal muscle regeneration / 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 / Specification of the neural plate border / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal root ganglion development / synaptic vesicle clustering / acinar cell differentiation / dorsal/ventral axis specification / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / layer formation in cerebral cortex / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / sympathetic ganglion development / fungiform papilla formation / lung epithelial cell differentiation / embryonic foregut morphogenesis / hindbrain development / regulation of calcium ion import / positive regulation of determination of dorsal identity / ectoderm development / positive regulation of skeletal muscle tissue development / cranial skeletal system development / regulation of protein localization to cell surface / hair cell differentiation / cellular response to indole-3-methanol / mesenchymal cell proliferation involved in lung development / endothelial tube morphogenesis / positive regulation of odontoblast differentiation / presynaptic active zone cytoplasmic component / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / alpha-catenin binding / establishment of blood-brain barrier / Germ layer formation at gastrulation / negative regulation of oligodendrocyte differentiation / male genitalia development / fascia adherens / flotillin complex / apicolateral plasma membrane / epithelial cell proliferation involved in prostate gland development / epithelial cell differentiation involved in prostate gland development / Formation of definitive endoderm / positive regulation of epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / embryonic brain development / beta-catenin destruction complex / oocyte development / adherens junction assembly / lung-associated mesenchyme development / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / Formation of axial mesoderm / negative regulation of protein sumoylation / cis-Golgi network / embryonic heart tube development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gupta, D. / Bienz, M. | ||||||
Citation | Journal: Nat Commun / Year: 2012 Title: An intrinsically labile alpha-helix abutting the BCL9-binding site of beta-catenin is required for its inhibition by carnosic acid. Authors: de la Roche, M. / Rutherford, T.J. / Gupta, D. / Veprintsev, D.B. / Saxty, B. / Freund, S.M. / Bienz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sl9.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sl9.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 3sl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3sl9 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sl9 | HTTPS FTP |
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-Related structure data
Related structure data | 3slaC 2gl7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ABEGCDFH
#1: Protein | Mass: 18176.174 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Beta catenin, CTNNB, CTNNB1, OK/SW-cl.35, PRO2286 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P35222 #2: Protein | Mass: 6171.756 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00512 |
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-Non-polymers , 5 types, 180 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-IMD / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 0.12M ethylene glycol, 1M MES 62% MES, 1M Imidazol 38%, 10% PEG 4K, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 20, 2009 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.07 Å / Num. obs: 54333 / % possible obs: 97.2 % / Observed criterion σ(I): -4 / Redundancy: 3.8 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 17.1 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GL7 Resolution: 2.2→29.43 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.251 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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