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- PDB-1ju5: Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, ... -

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Basic information

Entry
Database: PDB / ID: 1ju5
TitleTernary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy
Components
  • (Crk) x 2
  • Abl
KeywordsPROTEIN BINDING/TRANSFERASE / Crk / SH2 / Abl / SH3 / adaptor protein / phosphopeptide / PROTEIN BINDING-TRANSFERASE COMPLEX
Function / homology
Function and homology information


PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration / response to peptide / Downstream signal transduction / regulation of intracellular signal transduction / postsynaptic specialization assembly / protein phosphorylated amino acid binding / regulation of T cell migration / p130Cas linkage to MAPK signaling for integrins / reelin-mediated signaling pathway / negative regulation of phospholipase C activity / positive regulation of actin filament binding / regulation of dendrite development / positive regulation of oxidoreductase activity / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / podocyte apoptotic process / DN4 thymocyte differentiation / Role of ABL in ROBO-SLIT signaling / response to epinephrine / positive regulation of skeletal muscle acetylcholine-gated channel clustering / activation of protein kinase C activity / response to yeast / nicotinate-nucleotide adenylyltransferase activity / Regulation of signaling by CBL / regulation of modification of synaptic structure / regulation of Rac protein signal transduction / positive regulation of extracellular matrix organization / positive regulation of microtubule binding / delta-catenin binding / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / neuroepithelial cell differentiation / negative regulation of wound healing / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / mitochondrial depolarization / regulation of protein binding / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / negative regulation of cell motility / neuropilin binding / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / regulation of Cdc42 protein signal transduction / ARMS-mediated activation / activated T cell proliferation / cellular response to dopamine / VEGFA-VEGFR2 Pathway / MET receptor recycling / protein localization to membrane / regulation of cell motility / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / MET activates RAP1 and RAC1 / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / regulation of hematopoietic stem cell differentiation / cellular response to insulin-like growth factor stimulus / syntaxin binding / negative regulation of natural killer cell mediated cytotoxicity / cardiac muscle cell proliferation / HDR through Single Strand Annealing (SSA) / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / establishment of cell polarity / positive regulation of cell migration involved in sprouting angiogenesis / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / negative regulation of cell-cell adhesion / Myogenesis / dendrite development / regulation of microtubule polymerization / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / positive regulation of Rac protein signal transduction / RUNX2 regulates osteoblast differentiation / negative regulation of cellular senescence / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of long-term synaptic potentiation / regulation of cell adhesion mediated by integrin / Bergmann glial cell differentiation / associative learning
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 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 / Src homology 3 domains / SH2 domain / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase ABL1 / Adapter molecule crk / Adapter molecule crk
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / ARIA 1.0, CNS 1.0
AuthorsDonaldson, L.W. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide
Authors: Donaldson, L.W. / Gish, G. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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: Crk
B: Crk
C: Abl


Theoretical massNumber of molelcules
Total (without water)20,3763
Polymers20,3763
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Crk / PROTO-ONCOGENE C-CRK / ADAPTER MOLECULE CRK / P38


Mass: 12142.571 Da / Num. of mol.: 1 / Fragment: Crk SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P46108
#2: Protein/peptide Crk / PROTO-ONCOGENE C-CRK / ADAPTER MOLECULE CRK / P38


Mass: 1468.480 Da / Num. of mol.: 1 / Fragment: Crk phosphopeptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAED4-MMHB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q64010
#3: Protein Abl / proto-oncogene tyrosine-protein kinase


Mass: 6764.461 Da / Num. of mol.: 1 / Fragment: Abl SH3 domain / Mutation: L122K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00519, EC: 2.7.1.112

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1313D 13C F1-FILTERED F3-EDITED NOESY
141J-HNHA
151IPAP-15N HSQC
NMR detailsText: Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% ...Text: Intermolecular distance restraints were obtained from reverse half-filtered 2D- and 3D-NOESY spectra (300 ms mixing time) on sample in 99% D2O. Methyl prochiral assignments were made on a 10% 13C-labeled sample according to Neri et al (Biochemistry 28:7510; 1989). HACAN and CBCA(CO)N(CA)HA experiments were used to assign the proline residues in the Crk SH2 domain according to Kanelis et al (JBNMR 16:253; 2000)

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Sample preparation

DetailsContents: 0.6-1.5mM Crk SH2 domain U-15N, 13C; 50mM sodium phosphate pH6.8, 0.02% sodium azide
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM sodium phosphate / pH: 6.8 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 UNITYPLUSVarianUNITYPLUS6002
Varian UNITYPLUSVarianUNITYPLUS8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglioprocessing
PIPP4.3.2Garrettdata analysis
CNS1Brungerstructure solution
ARIA1Brungerstructure solution
ARIA1Brungerrefinement
RefinementMethod: ARIA 1.0, CNS 1.0 / Software ordinal: 1
Details: This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2- ...Details: This structure represents the lowest energy solution based on 2406 SH2 intramolecular restraints, 1628 SH3 intramolecular restraints, 37 SH2-SH3 intermolecular restraints, 64 SH2-phosphopeptide intermolecular restraints, 50 hydrogen bonds, 54 direct 3J-HNHA couplings and 166 dihedral angle restraints from TALOS Residues 217-220 and 225-229 of the Crk phosphopeptide (Chain B) are disordered. As intermolecular contacts between the SH2 domain (Chain A) and the SH3 domain (Chain C) limited to amino acids 67-75 in DE-loop of the SH2 domain, there is no unique orientation between the SH2 domain and SH3 domain.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 1

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