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Yorodumi- PDB-1wh4: Solution structure of the DEATH domain of Interleukin-1 receptor-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wh4 | ||||||
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Title | Solution structure of the DEATH domain of Interleukin-1 receptor-associated kinase4 (IRAK4) from Mus musculus | ||||||
Components | interleukin-1 receptor-associated kinase 4 | ||||||
Keywords | TRANSFERASE / DEATH domain / Structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Interleukin-1 signaling / Toll signaling pathway / PIP3 activates AKT signaling / neutrophil migration / interleukin-33-mediated signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / JNK cascade ...Interleukin-1 signaling / Toll signaling pathway / PIP3 activates AKT signaling / neutrophil migration / interleukin-33-mediated signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / JNK cascade / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / cell surface / magnesium ion binding / extracellular space / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Nameki, N. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the DEATH domain of Interleukin-1 receptor-associated kinase4 (IRAK4) from Mus musculus Authors: Nameki, N. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wh4.cif.gz | 753.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wh4.ent.gz | 632.8 KB | Display | PDB format |
PDBx/mmJSON format | 1wh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wh4_validation.pdf.gz | 356.7 KB | Display | wwPDB validaton report |
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Full document | 1wh4_full_validation.pdf.gz | 475.5 KB | Display | |
Data in XML | 1wh4_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 1wh4_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/1wh4 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/1wh4 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13769.712 Da / Num. of mol.: 1 / Fragment: DEATH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: RIKEN cDNA 9330209D03 / Plasmid: P021209-23 / References: UniProt: Q8R4K2, EC: 2.7.1.37 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.7mM DEATH domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.5); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.5 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |