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- PDB-2eyv: SH2 domain of CT10-Regulated Kinase -

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Basic information

Entry
Database: PDB / ID: 2eyv
TitleSH2 domain of CT10-Regulated Kinase
Componentsv-crk sarcoma virus CT10 oncogene homolog isoform a
KeywordsSIGNALING PROTEIN / SH2
Function / homology
Function and homology information


response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / regulation of intracellular signal transduction / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / response to peptide ...response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / regulation of intracellular signal transduction / response to cholecystokinin / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / response to peptide / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of natural killer cell mediated cytotoxicity / response to yeast / negative regulation of wound healing / reelin-mediated signaling pathway / negative regulation of cell motility / ARMS-mediated activation / protein localization to membrane / MET receptor recycling / MET activates RAP1 and RAC1 / regulation of GTPase activity / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / p130Cas linkage to MAPK signaling for integrins / enzyme-linked receptor protein signaling pathway / positive regulation of smooth muscle cell migration / dendrite development / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / ephrin receptor signaling pathway / cellular response to nitric oxide / regulation of signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / signaling adaptor activity / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / cytoskeletal protein binding / ephrin receptor binding / phosphotyrosine residue binding / Downstream signal transduction / SH2 domain binding / cell chemotaxis / protein tyrosine kinase binding / cellular response to nerve growth factor stimulus / hippocampus development / regulation of actin cytoskeleton organization / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / neuron migration / neuromuscular junction / lipid metabolic process / response to hydrogen peroxide / Regulation of actin dynamics for phagocytic cup formation / receptor tyrosine kinase binding / cerebral cortex development / kinase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / cell migration / actin cytoskeleton / signaling receptor complex adaptor activity / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / positive regulation of cell growth / cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Adapter molecule crk
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKobashigawa, Y. / Tanaka, S. / Inagaki, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for the transforming activity of human cancer-related signaling adaptor protein CRK.
Authors: Kobashigawa, Y. / Sakai, M. / Naito, M. / Yokochi, M. / Kumeta, H. / Makino, Y. / Ogura, K. / Tanaka, S. / Inagaki, F.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 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_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 29, 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: v-crk sarcoma virus CT10 oncogene homolog isoform a


Theoretical massNumber of molelcules
Total (without water)13,7501
Polymers13,7501
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)1 / 20
RepresentativeModel #1lowest energy

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Components

#1: Protein v-crk sarcoma virus CT10 oncogene homolog isoform a / CT10-Regulated Kinase


Mass: 13750.260 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPRO EX-htb / Production host: Escherichia coli (E. coli) / References: GenBank: 41327712, UniProt: P46108*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY

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Sample preparation

DetailsContents: 1.0MM SH2 U-15N, 13C PHOSPHATE BUFFER NA; 200MM NACL;90%H2O, 10%D2O
Sample conditionsIonic strength: 250mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guetntert P.refinement
XEASYstructure solution
Oliviastructure solution
NMRPipestructure solution
CYANA2Guetntert P.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 1

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