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- PDB-1z23: The serine-rich domain from Crk-associated substrate (p130Cas) -

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Basic information

Entry
Database: PDB / ID: 1z23
TitleThe serine-rich domain from Crk-associated substrate (p130Cas)
ComponentsCRK-associated substrate
KeywordsCELL ADHESION / four-helix bundle
Function / homology
Function and homology information


p130Cas linkage to MAPK signaling for integrins / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / VEGFA-VEGFR2 Pathway / Downstream signal transduction / antigen receptor-mediated signaling pathway / cellular response to endothelin / negative regulation of substrate adhesion-dependent cell spreading / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus ...p130Cas linkage to MAPK signaling for integrins / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / VEGFA-VEGFR2 Pathway / Downstream signal transduction / antigen receptor-mediated signaling pathway / cellular response to endothelin / negative regulation of substrate adhesion-dependent cell spreading / endothelin receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / cellular response to hepatocyte growth factor stimulus / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / ruffle / positive regulation of endothelial cell migration / cellular response to nitric oxide / cell surface receptor protein tyrosine kinase signaling pathway / actin filament organization / integrin-mediated signaling pathway / cell chemotaxis / B cell receptor signaling pathway / SH3 domain binding / epidermal growth factor receptor signaling pathway / insulin receptor signaling pathway / cell migration / lamellipodium / actin cytoskeleton / actin cytoskeleton organization / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / protein domain specific binding / axon / focal adhesion / protein kinase binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Serine-rich domain / 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 / SH3 domain ...Serine-rich domain / 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 / SH3 domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Breast cancer anti-estrogen resistance protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBriknarova, K. / Nasertorabi, F. / Havert, M.L. / Eggleston, E. / Hoyt, D.W. / Li, C. / Olson, A.J. / Vuori, K. / Ely, K.R.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: The serine-rich domain from Crk-associated substrate (p130cas) is a four-helix bundle.
Authors: Briknarova, K. / Nasertorabi, F. / Havert, M.L. / Eggleston, E. / Hoyt, D.W. / Li, C. / Olson, A.J. / Vuori, K. / Ely, K.R.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Cell adhesion regulates the interactions between the docking protein p130(Cas) and the 14-3-3 proteins
Authors: Garcia-Guzman, M. / Dolfi, F. / Russello, M. / Vuori, K.
History
DepositionMar 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRK-associated substrate


Theoretical massNumber of molelcules
Total (without water)17,3481
Polymers17,3481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 99structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CRK-associated substrate / p130cas / Breast cancer anti-estrogen resistance 1 protein


Mass: 17348.465 Da / Num. of mol.: 1 / Fragment: serine-rich domain, SRR-B, residues 546-708 / Mutation: V546G P547S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63767

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1324D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8mM protein U-15N, 20mM Tris U-2H, pH 7.9, 100mM NaCl, 5mM beta-mercaptoethanol, 1mM 4-(2-aminoethyl)benzene fluoride (AEBSF), 90% H2O, 10% D2O;90% H2O/10% D2O
21.8mM protein U-13C, U-15N, 20mM Tris U-2H, pH 7.9, 100mM NaCl, 5mM beta-mercaptoethanol, 1mM 4-(2-aminoethyl)benzene fluoride (AEBSF), 90% H2O, 10% D2O90% H2O/10% D2O
31.8mM protein U-13C, U-15N, ~60% 2H, 20mM Tris U-2H, pH 7.9, 100mM NaCl, 5mM beta-mercaptoethanol, 1mM 4-(2-aminoethyl)benzene fluoride (AEBSF), 90% H2O, 10% D2O90% H2O/10% D2O
41.8mM protein U-15N, ~60% 2H, 20mM Tris U-2H, pH 7.9, 100mM NaCl, 5mM beta-mercaptoethanol, 1mM 4-(2-aminoethyl)benzene fluoride (AEBSF), 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 0.1 / pH: 7.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrys, Inc., San Diego, CAprocessing
Felix2000Accelrys, Inc., San Diego, CAdata analysis
Xplor-NIH2.9.4aSchwieters et al.structure solution
Xplor-NIH2.9.4arefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The calculation employed a total of 1562 unambiguous distance restraints (166 long range, 245 medium range, 346 sequential and 805 intraresidual), 6 ambiguous long-range distance restraints, ...Details: The calculation employed a total of 1562 unambiguous distance restraints (166 long range, 245 medium range, 346 sequential and 805 intraresidual), 6 ambiguous long-range distance restraints, 176 hydrogen bond restraints, 107 phi and 107 psi dihedral angle restraints, and 79 residual dipolar coupling restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 99 / Conformers submitted total number: 20

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