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- PDB-5o2q: p130Cas SH3 domain Vinculin peptide chimera -

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Basic information

Entry
Database: PDB / ID: 5o2q
Titlep130Cas SH3 domain Vinculin peptide chimera
ComponentsBreast cancer anti-estrogen resistance 1,Vinculin
KeywordsSTRUCTURE FROM CYANA 3.97 / SH3 domain / p130Cas
Function / homology
Function and homology information


antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / alpha-catenin binding / cell-cell contact zone / hepatocyte growth factor receptor signaling pathway / podosome / cellular response to hepatocyte growth factor stimulus / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway ...antigen receptor-mediated signaling pathway / endothelin receptor signaling pathway / alpha-catenin binding / cell-cell contact zone / hepatocyte growth factor receptor signaling pathway / podosome / cellular response to hepatocyte growth factor stimulus / p130Cas linkage to MAPK signaling for integrins / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cell surface receptor protein tyrosine kinase signaling pathway / ruffle / positive regulation of endothelial cell migration / Downstream signal transduction / cell chemotaxis / actin filament organization / integrin-mediated signaling pathway / regulation of cell growth / adherens junction / B cell receptor signaling pathway / epidermal growth factor receptor signaling pathway / sarcolemma / beta-catenin binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / actin filament 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 / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Vinculin / Vinculin/alpha-catenin ...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 / Vinculin / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Vinculin / Breast cancer anti-estrogen resistance protein 1 / 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,Vinculin


Theoretical massNumber of molelcules
Total (without water)10,6231
Polymers10,6231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7350 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,Vinculin / CAS SH3 domain Vinculin peptide chimera


Mass: 10623.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCAR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P5Z4, UniProt: B4DKC9, UniProt: P56945*PLUS

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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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