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- PDB-2g57: Structure of the Phosphorylation Motif of the oncogenic Protein b... -

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Basic information

Entry
Database: PDB / ID: 2g57
TitleStructure of the Phosphorylation Motif of the oncogenic Protein beta-Catenin Recognized By a Selective Monoclonal Antibody
ComponentsBeta-catenin
KeywordsONCOPROTEIN / beta-Catenin oncogenic Protein / P-beta-Catenin phosphorylated peptide / epitope mapping / Antibody / P-beta-Catenin-Antibody complex / STD-NMR / TRNOESY / restrained molecular dynamics / bound structure / binding fragment
Function / homology
Function and homology information


positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic ...positive regulation of heparan sulfate proteoglycan biosynthetic process / cranial ganglion development / CDH11 homotypic and heterotypic interactions / embryonic skeletal limb joint morphogenesis / Regulation of CDH19 Expression and Function / astrocyte-dopaminergic neuron signaling / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / regulation of fibroblast proliferation / Scrib-APC-beta-catenin complex / beta-catenin-TCF complex / Specification of the neural plate border / positive regulation of skeletal muscle tissue development / synaptic vesicle clustering / Formation of the nephric duct / dorsal root ganglion development / endothelial tube morphogenesis / hindbrain development / mesenchymal to epithelial transition / cranial skeletal system development / sympathetic ganglion development / presynaptic active zone cytoplasmic component / regulation of protein localization to cell surface / fascia adherens / mesenchymal stem cell differentiation / detection of muscle stretch / positive regulation of odontoblast differentiation / alpha-catenin binding / cellular response to indole-3-methanol / regulation of epithelial to mesenchymal transition / regulation of calcium ion import / histone methyltransferase binding / hair cell differentiation / apicolateral plasma membrane / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / neuron projection extension / cell-cell adhesion mediated by cadherin / flotillin complex / Formation of definitive endoderm / regulation of smooth muscle cell proliferation / beta-catenin destruction complex / Formation of axial mesoderm / embryonic brain development / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / midbrain dopaminergic neuron differentiation / catenin complex / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of blood vessel branching / protein localization to cell surface / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / I-SMAD binding / Regulation of CDH1 Function / Adherens junctions interactions / Wnt signalosome / positive regulation of neuroblast proliferation / adherens junction assembly / Cardiogenesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / stem cell population maintenance / Myogenesis / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / hypothalamus development / Formation of paraxial mesoderm / regulation of synapse assembly / Somitogenesis / microvillus membrane / SMAD binding / outflow tract morphogenesis / canonical Wnt signaling pathway / Regulation of MITF-M-dependent genes involved in pigmentation / Transcriptional Regulation by VENTX / epithelial to mesenchymal transition / regulation of protein ubiquitination / regulation of angiogenesis / lateral plasma membrane / regulation of neurogenesis / bicellular tight junction / positive regulation of epithelial to mesenchymal transition / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / phosphatase binding / postsynaptic density, intracellular component / RHO GTPases activate IQGAPs / positive regulation of telomere maintenance via telomerase / negative regulation of angiogenesis / Transcriptional and post-translational regulation of MITF-M expression and activity
Similarity search - Function
Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Catenin beta-1 / Beta-catenin
Similarity search - Component
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsMegy, S. / Bertho, G. / Gharbi-Benarous, J. / Baleux, F. / Benarous, R. / Girault, J.P.
CitationJournal: Febs Lett. / Year: 2006
Title: STD and TRNOESY NMR studies for the epitope mapping of the phosphorylation motif of the oncogenic protein beta-catenin recognized by a selective monoclonal antibody
Authors: Megy, S. / Bertho, G. / Gharbi-Benarous, J. / Baleux, F. / Benarous, R. / Girault, J.P.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-catenin


Theoretical massNumber of molelcules
Total (without water)2,9291
Polymers2,9291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Beta-catenin


Mass: 2928.948 Da / Num. of mol.: 1 / Fragment: Residues 19-44 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P35222, UniProt: Q0PNE9*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 1mM P-beta-Cat peptide with 0.01mM antibody; 20mM phosphate buffered saline(pH 7.4); 15mM sodium azide; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM / pH: 7.4 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
Felixdata analysis
ARIA1.2refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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