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- PDB-3sla: X-ray structure of first four repeats of human beta-catenin -

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Basic information

Entry
Database: PDB / ID: 3sla
TitleX-ray structure of first four repeats of human beta-catenin
ComponentsCatenin beta-1
KeywordsSIGNALING PROTEIN / Beta Catenin / Armadillo repeat / Key component of the Wnt signaling pathway
Function / homology
Function and homology information


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 ...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 / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / 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 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / Binding of TCF/LEF:CTNNB1 to target gene promoters / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / lens morphogenesis in camera-type eye / Scrib-APC-beta-catenin complex / regulation of fibroblast proliferation / beta-catenin-TCF complex / acinar cell differentiation / synaptic vesicle clustering / dorsal root ganglion development / endodermal cell fate commitment / neuron fate determination / proximal/distal pattern formation / Formation of the nephric duct / endothelial tube morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / sympathetic ganglion development / dorsal/ventral axis specification / layer formation in cerebral cortex / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / fungiform papilla formation / mesenchymal to epithelial transition / hindbrain development / positive regulation of skeletal muscle tissue development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / fascia adherens / regulation of protein localization to cell surface / hair cell differentiation / ectoderm development / embryonic foregut morphogenesis / cellular response to indole-3-methanol / detection of muscle stretch / positive regulation of odontoblast differentiation / smooth muscle cell differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of myoblast proliferation / alpha-catenin binding / histone methyltransferase binding / 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 / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / cranial skeletal system development / cell-cell adhesion mediated by cadherin / male genitalia development / epithelial cell proliferation involved in prostate gland development / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / catenin complex / embryonic brain development / lung-associated mesenchyme development / oocyte development / beta-catenin destruction complex / establishment of blood-brain barrier / midbrain dopaminergic neuron differentiation / Formation of axial mesoderm / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / gastrulation with mouth forming second / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants
Similarity search - Function
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 / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Catenin beta-1
C: Catenin beta-1
D: Catenin beta-1
E: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,47915
Polymers91,6975
Non-polymers78310
Water1,54986
1
A: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7085
Polymers18,3391
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)18,3391
Polymers18,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)18,3391
Polymers18,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5243
Polymers18,3391
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Catenin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5705
Polymers18,3391
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.790, 90.790, 364.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 18339.348 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Beta catenin, CTNNB, CTNNB1, OK/SW-cl.35, PRO2286 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P35222
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.09 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.98M sodium acetate trihydrate, 30% glycerol, 0.07M sodium cacodylate, 30% w/v galactose , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.93 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2010
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→64.51 Å / Num. obs: 50802 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 5.7 % / Biso Wilson estimate: 58.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.565 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 11.1 / Num. unique all: 53715 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.869 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27705 2719 5.1 %RANDOM
Rwork0.21823 ---
obs0.22115 50802 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 50 86 6074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226047
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9738179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.26624.524210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.946151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1311530
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214269
X-RAY DIFFRACTIONr_mcbond_it4.74153979
X-RAY DIFFRACTIONr_mcangle_it6.87366359
X-RAY DIFFRACTIONr_scbond_it6.47752068
X-RAY DIFFRACTIONr_scangle_it9.3037.51820
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 210 -
Rwork0.338 3644 -
obs--99.05 %

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