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- PDB-3sl9: X-ray structure of Beta catenin in complex with Bcl9 -

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Basic information

Entry
Database: PDB / ID: 3sl9
TitleX-ray structure of Beta catenin in complex with Bcl9
Components
  • B-cell CLL/lymphoma 9 protein
  • Catenin beta-1
KeywordsSIGNALING 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 / embryonic axis specification / endodermal cell fate commitment / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / positive regulation of fibroblast growth factor receptor signaling pathway / beta-catenin-TCF complex / lens morphogenesis in camera-type eye / dorsal root ganglion development / synaptic vesicle clustering / 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 / mesenchymal cell proliferation involved in lung development / detection of muscle stretch / smooth muscle cell differentiation / histone methyltransferase binding / midbrain dopaminergic neuron differentiation / presynaptic active zone cytoplasmic component / alpha-catenin binding / cellular response to indole-3-methanol / flotillin complex / Germ layer formation at gastrulation / establishment of blood-brain barrier / male genitalia development / negative regulation of oligodendrocyte differentiation / apicolateral plasma membrane / fascia adherens / epithelial cell proliferation involved in prostate gland development / 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 / cis-Golgi network / negative regulation of protein sumoylation / adherens junction assembly / embryonic heart tube 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
Similarity search - Function
B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / 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 ...B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / B-cell CLL/lymphoma 9 protein / Catenin beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGupta, D. / Bienz, M.
CitationJournal: 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
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Sep 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
C: B-cell CLL/lymphoma 9 protein
B: Catenin beta-1
D: B-cell CLL/lymphoma 9 protein
E: Catenin beta-1
F: B-cell CLL/lymphoma 9 protein
G: Catenin beta-1
H: B-cell CLL/lymphoma 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,54936
Polymers97,3928
Non-polymers2,15728
Water2,738152
1
A: Catenin beta-1
C: B-cell CLL/lymphoma 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,94710
Polymers24,3482
Non-polymers5998
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-4 kcal/mol
Surface area9920 Å2
MethodPISA
2
B: Catenin beta-1
D: B-cell CLL/lymphoma 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,00010
Polymers24,3482
Non-polymers6528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-6 kcal/mol
Surface area9210 Å2
MethodPISA
3
E: Catenin beta-1
F: B-cell CLL/lymphoma 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,95610
Polymers24,3482
Non-polymers6088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-5 kcal/mol
Surface area10450 Å2
MethodPISA
4
G: Catenin beta-1
H: B-cell CLL/lymphoma 9 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6476
Polymers24,3482
Non-polymers2994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.890, 80.700, 87.940
Angle α, β, γ (deg.)90.00, 102.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 8 molecules ABEGCDFH

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


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
B-cell CLL/lymphoma 9 protein / / B-cell lymphoma 9 protein / Bcl-9 / Protein legless homolog


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 / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 20, 2009
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 17.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GL7

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
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2763 5.1 %RANDOM
Rwork0.194 ---
obs0.197 51571 97 %-
all-51571 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 144 152 5813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0215708
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9777660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.20424.158202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64315977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.431533
X-RAY DIFFRACTIONr_chiral_restr0.160.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024039
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.28453706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.86165887
X-RAY DIFFRACTIONr_scbond_it6.42352002
X-RAY DIFFRACTIONr_scangle_it9.097.51773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 205 -
Rwork0.206 3765 -
obs--96.5 %

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