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- PDB-1jpp: The Structure of a beta-Catenin Binding Repeat from Adenomatous P... -

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Basic information

Entry
Database: PDB / ID: 1jpp
TitleThe Structure of a beta-Catenin Binding Repeat from Adenomatous Polyposis Coli (APC) in Complex with beta-Catenin
Components
  • ADENOMATOUS POLYPOSIS COLI PROTEINFamilial adenomatous polyposis
  • BETA-CATENINCatenin beta-1
KeywordsCELL ADHESION / Disease mutation / Anti-oncogene
Function / homology
Function and homology information


lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / : / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / APC truncation mutants are not K63 polyubiquitinated / Disassembly of the destruction complex and recruitment of AXIN to the membrane ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / : / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Beta-catenin phosphorylation cascade / APC truncation mutants are not K63 polyubiquitinated / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Apoptotic cleavage of cell adhesion proteins / hair cycle process / positive regulation of epithelial cell differentiation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / TCF dependent signaling in response to WNT / mesenchyme development / Formation of the beta-catenin:TCF transactivating complex / trachea morphogenesis / endoderm formation / 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 / VEGFR2 mediated vascular permeability / neural plate development / Deactivation of the beta-catenin transactivating complex / glial cell fate determination / animal organ development / regulation of microtubule-based movement / 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 / central nervous system vasculogenesis / Ca2+ pathway / regulation of epithelial cell differentiation / Schwann cell proliferation / regulation of centriole-centriole cohesion / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / Degradation of beta-catenin by the destruction complex / negative regulation of cell cycle G1/S phase transition / RHO GTPases activate IQGAPs / Adherens junctions interactions / embryonic axis specification / endodermal cell fate commitment / ventricular compact myocardium morphogenesis / Scrib-APC-beta-catenin complex / morphogenesis of embryonic epithelium / 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 / sympathetic ganglion development / positive regulation of myoblast proliferation / positive regulation of endothelial cell differentiation / establishment of blood-retinal barrier / fungiform papilla formation / lung epithelial cell differentiation / gamma-catenin binding / embryonic foregut morphogenesis / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / delta-catenin binding / 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 / regulation of osteoclast differentiation / cranial skeletal system development / endothelial tube morphogenesis / regulation of protein localization to cell surface / mesenchymal cell proliferation involved in lung development / smooth muscle cell differentiation / midbrain dopaminergic neuron differentiation / histone methyltransferase binding / presynaptic active zone cytoplasmic component / cell projection membrane
Similarity search - Function
Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding ...Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / 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
Adenomatous polyposis coli protein / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSpink, K.E. / Fridman, S.G. / Weis, W.I.
Citation
Journal: EMBO J. / Year: 2001
Title: Molecular mechanisms of beta-catenin recognition by adenomatous polyposis coli revealed by the structure of an APC-beta-catenin complex.
Authors: Eklof Spink, K. / Fridman, S.G. / Weis, W.I.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The structure of the beta-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by beta-catenin
Authors: Huber, A.H. / Weis, W.I.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: CRYSTAL STRUCTURE OF A BETA-CATENIN/TCF COMPLEX
Authors: Graham, T.A. / Weaver, C. / Mao, F. / Kimelman, D. / Xu, W.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: THREE-DIMENSIONAL STRUCTURE OF THE ARMADILLO REPEAT REGION OF BETA-CATENIN
Authors: Huber, A.H. / Nelson, W.J. / Weis, W.I.
History
DepositionAug 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: BETA-CATENIN
B: BETA-CATENIN
C: ADENOMATOUS POLYPOSIS COLI PROTEIN
D: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3545
Polymers121,2624
Non-polymers921
Water1,29772
1
A: BETA-CATENIN
C: ADENOMATOUS POLYPOSIS COLI PROTEIN


Theoretical massNumber of molelcules
Total (without water)60,6312
Polymers60,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-CATENIN
D: ADENOMATOUS POLYPOSIS COLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7233
Polymers60,6312
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.090, 69.255, 95.099
Angle α, β, γ (deg.)68.70, 87.04, 85.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BETA-CATENIN / Catenin beta-1


Mass: 58844.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q02248
#2: Protein/peptide ADENOMATOUS POLYPOSIS COLI PROTEIN / Familial adenomatous polyposis / APC PROTEIN


Mass: 1786.911 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P25054
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, sodium potassium phosphate, sodium chloride, DTT, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %PEG80001reservoir
2100 mMsodium potassium phosphate1reservoirpH6.2
3200 mM1reservoirNaCl
45 mMdithiothreitol1reservoir
50.075 mMbeta-catenin1drop
60.092 mMAPC-rA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2001
RadiationMonochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→28.3 Å / Num. all: 21958 / Num. obs: 19916 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 1.47 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.082
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1.39 % / Rmerge(I) obs: 0.242 / Num. unique all: 1937 / % possible all: 87.8
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G3J

1g3j


Resolution: 3.1→28.27 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1211274.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 971 5.1 %RANDOM
Rwork0.234 ---
obs0.234 18919 86.1 %-
all-21958 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.503 Å2 / ksol: 0.320417 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.81 Å21.12 Å20.44 Å2
2--8.52 Å23.59 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.1→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7772 0 6 72 7850
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.394 107 6.2 %
Rwork0.347 1613 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.394 / % reflection Rfree: 6.2 % / Rfactor Rwork: 0.347

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