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- PDB-1qz7: Beta-catenin binding domain of Axin in complex with beta-catenin -

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Basic information

Entry
Database: PDB / ID: 1qz7
TitleBeta-catenin binding domain of Axin in complex with beta-catenin
Components
  • Axin
  • Beta-catenin
KeywordsCELL ADHESION / Beta-catenin / Axin / protein-protein complex
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 / cell development / 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 / detection of muscle stretch / cellular response to indole-3-methanol / 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 calcium ion import / regulation of epithelial to mesenchymal transition / 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 / beta-catenin destruction complex / lung-associated mesenchyme development / oocyte development / midbrain dopaminergic neuron differentiation / establishment of blood-brain barrier / 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 / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Beta-catenin / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / 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 / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Catenin beta-1 / Axin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXing, Y. / Clements, W.K. / Kimelman, D. / Xu, W.
CitationJournal: GENES DEV. / Year: 2003
Title: Crystal structure of a beta-catenin/Axin complex suggests a mechanism for the {beta}-catenin destruction complex
Authors: Xing, Y. / Clements, W.K. / Kimelman, D. / Xu, W.
History
DepositionSep 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-catenin
B: Axin


Theoretical massNumber of molelcules
Total (without water)65,9682
Polymers65,9682
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-9 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.141, 75.041, 101.398
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-catenin / PRO2286


Mass: 58211.438 Da / Num. of mol.: 1 / Fragment: Armadillo repeat region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNB1 / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P35222
#2: Protein Axin / Axis inhibition protein / xAxin


Mass: 7756.588 Da / Num. of mol.: 1 / Fragment: Beta-catenin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: AXIN / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: Q9YGY0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 6000, sodium citrate, isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
220 mMTris1droppH8.5
30.15 M1dropNaCl
42 mMdithiothreitol1drop
50.1 Msodium citrate1reservoirpH5.6
615 %(v/v)isopropanol1reservoir
77 %(w/v)PEG4000-60001reservoir
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 37253 / Num. obs: 37253 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3651 / Rsym value: 0.702 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I7X

1i7x


Resolution: 2.2→42.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 267694.88 / Data cutoff high rms absF: 267694.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1310 5 %RANDOM
Rwork0.221 ---
obs0.221 26204 81.1 %-
all-26204 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.402 Å2 / ksol: 0.345268 e/Å3
Displacement parametersBiso mean: 54.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å28.65 Å2
2--0.36 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-50 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 0 31 4148
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_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 147 5 %
Rwork0.235 2795 -
obs-2942 55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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