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- PDB-2dvj: phosphorylated Crk-II -

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Basic information

Entry
Database: PDB / ID: 2dvj
Titlephosphorylated Crk-II
ComponentsV-crk sarcoma virus CT10 oncogene homolog, isoform a
KeywordsSIGNALING PROTEIN / SH3 / SH2 / signal transduction / adapter molecule
Function / homology
Function and homology information


response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of intracellular signal transduction / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / reelin-mediated signaling pathway ...response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of intracellular signal transduction / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / reelin-mediated signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / response to yeast / negative regulation of wound healing / regulation of protein binding / negative regulation of cell motility / ARMS-mediated activation / MET receptor recycling / protein localization to membrane / MET activates RAP1 and RAC1 / cellular response to insulin-like growth factor stimulus / negative regulation of natural killer cell mediated cytotoxicity / establishment of cell polarity / regulation of GTPase activity / p130Cas linkage to MAPK signaling for integrins / dendrite development / positive regulation of smooth muscle cell migration / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / cellular response to nitric oxide / ephrin receptor signaling pathway / regulation of signal transduction / signaling adaptor activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / insulin-like growth factor receptor binding / protein tyrosine kinase binding / cytoskeletal protein binding / SH2 domain binding / phosphotyrosine residue binding / ephrin receptor binding / cell chemotaxis / Downstream signal transduction / cellular response to nerve growth factor stimulus / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / hippocampus development / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / neuron migration / neuromuscular junction / response to hydrogen peroxide / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / kinase binding / VEGFA-VEGFR2 Pathway / : / cell migration / signaling receptor complex adaptor activity / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / positive regulation of cell growth / scaffold protein binding / cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / signal transduction / 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 Domains / 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 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Adapter molecule crk / Adapter molecule crk
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKobashigawa, Y. / 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
DepositionJul 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)25,5251
Polymers25,5251
Non-polymers00
Water0
1


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

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Components

#1: Protein V-crk sarcoma virus CT10 oncogene homolog, isoform a / V-crk sarcoma virus CT10 oncogene homolog / Avian / phosphorylated Crk-II


Mass: 25525.066 Da / Num. of mol.: 1 / Fragment: residues 1-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRK / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: Q96HJ0, UniProt: P46108*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.8mM pYCrk-II (1-228) U-15N,13C; 200mM NaCl, 50mM phosphate buffer NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert Pstructure solution
CNS1.1Brunger ATrefinement
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 1

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