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Yorodumi- PDB-1k76: Solution Structure of the C-terminal Sem-5 SH3 Domain (Minimized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k76 | ||||||
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Title | Solution Structure of the C-terminal Sem-5 SH3 Domain (Minimized Average Structure) | ||||||
Components | SEX MUSCLE ABNORMAL PROTEIN 5 | ||||||
Keywords | SIGNALING PROTEIN / all beta protein | ||||||
Function / homology | Function and homology information Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / : / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / PI-3K cascade:FGFR4 / RHO GTPases Activate WASPs and WAVEs / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR downregulation / PI3K events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / Negative regulation of MET activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Cargo recognition for clathrin-mediated endocytosis / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / regulation of nematode larval development / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / muscle organ development / epidermal growth factor receptor binding / regulation of MAPK cascade / regulation of cell migration / phosphotyrosine residue binding / epidermal growth factor receptor signaling pathway / signal transduction / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing, molecular dynamics | ||||||
Model type details | minimized average | ||||||
Authors | Ferreon, J. / Volk, D. / Luxon, B. / Gorenstein, D. / Hilser, V. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Solution Structure, Dynamics and Thermodynamics of the Native State Ensemble of Sem-5 C-Terminal SH3 Domain Authors: Ferreon, J. / Volk, D. / Luxon, B. / Gorenstein, D. / Hilser, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k76.cif.gz | 32.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k76.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k76 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k76 | HTTPS FTP |
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-Related 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: 7237.967 Da / Num. of mol.: 1 / Fragment: SH3 domain (Residues 155-214) / Mutation: C57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Sem-5 / Plasmid: pET19B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: P29355 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details | Contents: 13C,15N 1mM Sem-5 SH3 domain 50 mM sodium acetate buffer, 10 mM CaCl2, 100 mM NaCl,pH 4.8, 90%h20, 10%d20 Solvent system: 90%h20, 10%d20 |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 4.8 / Pressure: ambient / Temperature: 298 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 | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 400 MHz |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||
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NMR software |
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Refinement | Method: distance geometry simulated annealing, molecular dynamics Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 1 |