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- PDB-5o2p: p130Cas SH3 domain PTP-PEST peptide chimera -

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Basic information

Entry
Database: PDB / ID: 5o2p
Titlep130Cas SH3 domain PTP-PEST peptide chimera
ComponentsBreast cancer anti-estrogen resistance 1,Tyrosine-protein phosphatase non-receptor type 12
KeywordsSTRUCTURE FROM CYANA 3.97 / SH3 domain / p130Cas
Function / homology
Function and homology information


negative regulation of platelet-derived growth factor receptor-beta signaling pathway / antigen receptor-mediated signaling pathway / negative regulation of ERBB signaling pathway / regulation of epidermal growth factor receptor signaling pathway / endothelin receptor signaling pathway / tissue regeneration / Signaling by PDGF / hepatocyte growth factor receptor signaling pathway / Interleukin-37 signaling / podosome ...negative regulation of platelet-derived growth factor receptor-beta signaling pathway / antigen receptor-mediated signaling pathway / negative regulation of ERBB signaling pathway / regulation of epidermal growth factor receptor signaling pathway / endothelin receptor signaling pathway / tissue regeneration / Signaling by PDGF / hepatocyte growth factor receptor signaling pathway / Interleukin-37 signaling / podosome / cellular response to hepatocyte growth factor stimulus / p130Cas linkage to MAPK signaling for integrins / phosphoprotein phosphatase activity / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cellular response to epidermal growth factor stimulus / ruffle / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of endothelial cell migration / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / protein dephosphorylation / protein-tyrosine-phosphatase / cell chemotaxis / protein tyrosine phosphatase activity / cell projection / integrin-mediated signaling pathway / regulation of cell growth / actin filament organization / EGFR downregulation / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / SH3 domain binding / cell migration / actin cytoskeleton / insulin receptor signaling pathway / lamellipodium / T cell receptor signaling pathway / regulation of apoptotic process / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / cell division / axon / focal adhesion / protein kinase binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-12 / : / : / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain ...Protein-tyrosine phosphatase, non-receptor type-12 / : / : / BCAR1, SH3 domain / Serine rich protein interaction domain / CAS family, C-terminal / CAS family / CAS, serine rich four helix bundle domain superfamily / Serine rich protein interaction domain / Crk-Associated Substrate C-terminal domain / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Breast cancer anti-estrogen resistance protein 1 / Tyrosine-protein phosphatase non-receptor type 12 / Breast cancer anti-estrogen resistance 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHexnerova, R. / Veverka, V.
CitationJournal: Sci Rep / Year: 2017
Title: Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners.
Authors: Gemperle, J. / Hexnerova, R. / Lepsik, M. / Tesina, P. / Dibus, M. / Novotny, M. / Brabek, J. / Veverka, V. / Rosel, D.
History
DepositionMay 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3Jun 19, 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: Breast cancer anti-estrogen resistance 1,Tyrosine-protein phosphatase non-receptor type 12


Theoretical massNumber of molelcules
Total (without water)10,8471
Polymers10,8471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7580 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Breast cancer anti-estrogen resistance 1,Tyrosine-protein phosphatase non-receptor type 12 / CAS SH3 domain PTP-PEST peptide chimera / PTP-PEST / Protein-tyrosine phosphatase G1 / PTPG1 / CAS ...CAS SH3 domain PTP-PEST peptide chimera / PTP-PEST / Protein-tyrosine phosphatase G1 / PTPG1 / CAS SH3 domain PTP-PEST peptide chimera


Mass: 10847.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAR1, PTPN12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P5Z4, UniProt: Q05209, UniProt: P56945*PLUS, protein-tyrosine-phosphatase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 25 mM sodium phosphate, 1 M TCEP, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphatenatural abundance1
1 MTCEPnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKriegerrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40

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