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- PDB-2lqw: Solution structure of phosphorylated CRKL -

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Basic information

Entry
Database: PDB / ID: 2lqw
TitleSolution structure of phosphorylated CRKL
ComponentsCrk-like protein
KeywordsSIGNALING PROTEIN / SH2 / SH3 / v-crk sarcoma virus CT10 / oncogene homolog / (avian)-like / pCRKL
Function / homology
Function and homology information


positive regulation of glial cell migration / chordate pharynx development / extrinsic component of postsynaptic membrane / helper T cell diapedesis / cerebellar neuron development / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / reelin-mediated signaling pathway ...positive regulation of glial cell migration / chordate pharynx development / extrinsic component of postsynaptic membrane / helper T cell diapedesis / cerebellar neuron development / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / reelin-mediated signaling pathway / endothelin receptor signaling pathway / regulation of dendrite development / positive regulation of skeletal muscle acetylcholine-gated channel clustering / cranial skeletal system development / B cell apoptotic process / MET receptor recycling / cellular response to interleukin-7 / acetylcholine receptor signaling pathway / MET activates RAP1 and RAC1 / anterior/posterior pattern specification / Frs2-mediated activation / establishment of cell polarity / blood vessel development / dendrite development / outflow tract morphogenesis / positive regulation of Rac protein signal transduction / single fertilization / regulation of cell adhesion mediated by integrin / retinoic acid receptor signaling pathway / fibroblast growth factor receptor signaling pathway / signaling adaptor activity / Erythropoietin activates RAS / positive regulation of substrate adhesion-dependent cell spreading / JNK cascade / cellular response to transforming growth factor beta stimulus / phosphotyrosine residue binding / cell chemotaxis / Downstream signal transduction / thymus development / negative regulation of protein phosphorylation / regulation of cell growth / Regulation of signaling by CBL / hippocampus development / neuron migration / neuromuscular junction / lipid metabolic process / receptor tyrosine kinase binding / cerebral cortex development / male gonad development / cell migration / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / spermatogenesis / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / cadherin binding / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / signal transduction / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / cytosol
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 / SH3 type barrels. / Src homology 3 domains / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsJankowski, W. / Saleh, T. / Kalodimos, C.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Domain organization differences explain Bcr-Abl's preference for CrkL over CrkII.
Authors: Jankowski, W. / Saleh, T. / Pai, M.T. / Sriram, G. / Birge, R.B. / Kalodimos, C.G.
History
DepositionMar 16, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crk-like protein


Theoretical massNumber of molelcules
Total (without water)33,8971
Polymers33,8971
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)20 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Crk-like protein


Mass: 33896.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRKL / Production host: Escherichia coli (E. coli) / References: UniProt: P46109

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.3-0.8 mM [U-100% 15N] potassium phosphate, 0.3-0.8 mM [U-100% 13C; U-100% 15N] potassium chloride, 0.3-0.8 mM [U-13C; U-15N; U-2H] beta-mercaptoethanol, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMpotassium phosphate-1[U-100% 15N]0.3-0.81
mMpotassium chloride-2[U-100% 13C; U-100% 15N]0.3-0.81
mMbeta-mercaptoethanol-3[U-13C; U-15N; U-2H]0.3-0.81
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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