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- PDB-5uke: NMR structure of monomeric human IRAK-M Death Domain R56D, Y61E mutant -

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Basic information

Entry
Database: PDB / ID: 5uke
TitleNMR structure of monomeric human IRAK-M Death Domain R56D, Y61E mutant
ComponentsInterleukin-1 receptor-associated kinase 3
KeywordsTRANSFERASE / 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 protein-containing complex disassembly / response to peptidoglycan / negative regulation of macrophage cytokine production / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / interleukin-1-mediated signaling pathway ...positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of protein-containing complex disassembly / response to peptidoglycan / negative regulation of macrophage cytokine production / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor 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 MAP kinase activity / negative regulation of canonical NF-kappaB signal transduction / response to interleukin-1 / negative regulation of innate immune response / lipopolysaccharide-mediated signaling pathway / positive regulation of cytokine production / cytokine-mediated signaling pathway / negative regulation of protein catabolic process / response to virus / Interleukin-1 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / protein phosphorylation / protein heterodimerization activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 3, pseudokinase domain / IRAK3, death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Interleukin-1 receptor-associated kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsKwon, J. / Nicholson, L.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL111430 United States
CitationJournal: 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
DepositionJan 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase 3


Theoretical massNumber of molelcules
Total (without water)13,4671
Polymers13,4671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Interleukin-1 receptor-associated kinase 3 / IRAK-3 / IL-1 receptor-associated kinase M / IRAK-M


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D C(CO)NH
151isotropic13D HNCO
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HN(CO)CA
1121isotropic13D H(CCO)NH
1111isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-15N NOESY
191isotropic13D 1H-15N TOCSY
1131isotropic13D 1H-13C NOESY aliphatic
1141isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMIRAK-M Death Domain_R56D_Y61E[U-99% 13C; U-99% 15N]1
20 mMsodium chloridenatural abundance1
5 mMTCEPnatural abundance1
10 mMTRISnatural abundance1
5 mMsodium azidenatural abundance1
Sample conditionsIonic strength: 0.0229 M / Label: 13C_15N_sample / pH: 6.67 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
PINE2Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.115Goddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PONDEROSANMRFAM (University of Wisconsin-Madison), WoongHee Leerefinement
PONDEROSANMRFAM (University of Wisconsin-Madison), WoongHee Leestructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 4 / Details: NIH-Xplor imbedded to Ponderosa
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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