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Yorodumi- PDB-1ju5: Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ju5 | ||||||
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Title | Ternary complex of an Crk SH2 domain, Crk-derived phophopeptide, and Abl SH3 domain by NMR spectroscopy | ||||||
Components |
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Keywords | PROTEIN 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 / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / 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 / RUNX2 regulates osteoblast differentiation / positive regulation of Rac protein signal transduction / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / regulation of cell adhesion mediated by integrin / Bergmann glial cell differentiation / associative learning Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / ARIA 1.0, CNS 1.0 | ||||||
Authors | Donaldson, L.W. / Pawson, T. / Kay, L.E. / Forman-Kay, J.D. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ju5.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ju5.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ju5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1ju5 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1ju5 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein/peptide | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | 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% ...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) |
-Sample preparation
Details | Contents: 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 |
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Sample conditions | Ionic strength: 50mM sodium phosphate / pH: 6.8 / Pressure: ambient / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 1 |