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- PDB-2z6h: Crystal Structure of Beta-Catenin Armadillo Repeat Region and Its... -

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Basic information

Entry
Database: PDB / ID: 2z6h
TitleCrystal Structure of Beta-Catenin Armadillo Repeat Region and Its C-Terminal domain
ComponentsCatenin beta-1
KeywordsCELL ADHESION / Beta-Catenin / C-terminal Domain / Activator / Alternative splicing / Cytoplasm / Cytoskeleton / Disease mutation / Nucleus / Phosphorylation / Polymorphism / Structural protein / Transcription / Transcription regulation / Ubl conjugation / Wnt signaling pathway
Function / homology
Function and homology information


canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / 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 ...canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / 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 / 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 / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal/ventral axis specification / sympathetic ganglion development / lung epithelial cell differentiation / presynaptic active zone cytoplasmic component / positive regulation of endothelial cell differentiation / 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 / flotillin complex / male genitalia development / 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 / embryonic brain development / establishment of blood-brain barrier / Formation of axial mesoderm / beta-catenin destruction complex / negative regulation of protein sumoylation / catenin complex / Apoptotic cleavage of cell adhesion proteins / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / gastrulation with mouth forming second / positive regulation of blood vessel branching / embryonic heart tube development / pancreas development
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 / SIRAS / Resolution: 2.2 Å
AuthorsXing, Y. / Takemaru, K. / Liu, J. / Zheng, J. / Moon, R. / Xu, W.
CitationJournal: Structure / Year: 2008
Title: Crystal Structure of a Full-Length beta-Catenin
Authors: Xing, Y. / Takemaru, K. / Liu, J. / Berndt, J.D. / Zheng, J.J. / Moon, R.T. / Xu, W.
History
DepositionAug 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)70,4181
Polymers70,4181
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catenin beta-1

A: Catenin beta-1

A: Catenin beta-1

A: Catenin beta-1


Theoretical massNumber of molelcules
Total (without water)281,6714
Polymers281,6714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area10300 Å2
ΔGint-41 kcal/mol
Surface area83230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.229, 104.229, 259.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 70417.734 Da / Num. of mol.: 1
Fragment: Armadillo Repeat Region and C-terminal Domain (UNP residues 138-781)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: P35222
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na Citrate, 0.4M NaCl, 7% JEFFAMINE ED-2001, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00723, 1.07156
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.007231
21.071561
ReflectionResolution: 2.2→50 Å / Num. all: 35615 / Num. obs: 29790 / % possible obs: 81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2934 / Rsym value: 0.611 / % possible all: 81.2

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→48.69 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 369935.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2376 8 %RANDOM
Rwork0.213 ---
obs0.213 29783 80.9 %-
all-35615 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.16 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--2.79 Å20 Å2
3----5.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-50 Å
Luzzati sigma a0.24 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 0 28 4058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.422.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 243 7.9 %
Rwork0.27 2829 -
obs-2829 51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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