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Yorodumi- PDB-5uke: NMR structure of monomeric human IRAK-M Death Domain R56D, Y61E mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uke | ||||||
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Title | NMR structure of monomeric human IRAK-M Death Domain R56D, Y61E mutant | ||||||
Components | Interleukin-1 receptor-associated kinase 3 | ||||||
Keywords | TRANSFERASE / IRAK-M / Death Domain / Innate immunity / Asthma | ||||||
Function / homology | Function and homology information positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of macrophage cytokine production / negative regulation of protein-containing complex disassembly / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / MyD88-dependent toll-like receptor signaling pathway ...positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of macrophage cytokine production / negative regulation of protein-containing complex disassembly / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of NF-kappaB transcription factor activity / response to exogenous dsRNA / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of innate immune response / response to interleukin-1 / negative regulation of MAP kinase activity / positive regulation of cytokine production / response to virus / negative regulation of protein catabolic process / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / response to lipopolysaccharide / intracellular signal transduction / protein heterodimerization activity / protein phosphorylation / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Authors | Kwon, J. / Nicholson, L.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: The IL-33-PIN1-IRAK-M axis is critical for type 2 immunity in IL-33-induced allergic airway inflammation. Authors: Nechama, M. / Kwon, J. / Wei, S. / Kyi, A.T. / Welner, R.S. / Ben-Dov, I.Z. / Arredouani, M.S. / Asara, J.M. / Chen, C.H. / Tsai, C.Y. / Nelson, K.F. / Kobayashi, K.S. / Israel, E. / Zhou, X. ...Authors: Nechama, M. / Kwon, J. / Wei, S. / Kyi, A.T. / Welner, R.S. / Ben-Dov, I.Z. / Arredouani, M.S. / Asara, J.M. / Chen, C.H. / Tsai, C.Y. / Nelson, K.F. / Kobayashi, K.S. / Israel, E. / Zhou, X.Z. / Nicholson, L.K. / Lu, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uke.cif.gz | 724.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uke.ent.gz | 606.7 KB | Display | PDB format |
PDBx/mmJSON format | 5uke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uke_validation.pdf.gz | 407 KB | Display | wwPDB validaton report |
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Full document | 5uke_full_validation.pdf.gz | 546.4 KB | Display | |
Data in XML | 5uke_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 5uke_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/5uke ftp://data.pdbj.org/pub/pdb/validation_reports/uk/5uke | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13467.164 Da / Num. of mol.: 1 / Fragment: Death domain (UNP residues 1-119) / Mutation: R61D,Y66E Source method: isolated from a genetically manipulated source Details: hIRAKM 1-119 R56D,Y61E / Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK3 / Plasmid: pMAL-c2X Details (production host): N-terminal fusion partner MBP, separated by a Factor XA cleavage site Cell (production host): BL21(DE3) Gold / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y616, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 800 uM [U-99% 13C; U-99% 15N] IRAK-M Death Domain_R56D_Y61E, 20 mM sodium chloride, 5 mM TCEP, 10 mM TRIS, 5 mM sodium azide, 90% H2O/10% D2O Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.0229 M / Label: 13C_15N_sample / pH: 6.67 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 4 / Details: NIH-Xplor imbedded to Ponderosa | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |