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- PDB-2a9i: Molecular Structure of the Interleukin-1 Receptor-Associated Kina... -

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Basic information

Entry
Database: PDB / ID: 2a9i
TitleMolecular Structure of the Interleukin-1 Receptor-Associated Kinase-4 Death Domain
ComponentsInterleukin-1 receptor-associated kinase-4Interleukin-1 receptor associated kinase
KeywordsTRANSFERASE / hexahelical bundle
Function / homology
Function and homology information


Toll signaling pathway / Interleukin-1 signaling / 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 ...Toll signaling pathway / Interleukin-1 signaling / 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 / kinase activity / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / cell surface / extracellular space / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsLasker, M.V. / Gajjar, M.M. / Nair, S.K.
CitationJournal: J.Immunol. / Year: 2005
Title: Cutting Edge: Molecular Structure of the IL-1R-Associated Kinase-4 Death Domain and Its Implications for TLR Signaling.
Authors: Lasker, M.V. / Gajjar, M.M. / Nair, S.K.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7202
Polymers12,6651
Non-polymers551
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.152, 38.043, 51.588
Angle α, β, γ (deg.)90.00, 121.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-115-

HOH

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Components

#1: Protein Interleukin-1 receptor-associated kinase-4 / Interleukin-1 receptor associated kinase / IRAK-4


Mass: 12664.657 Da / Num. of mol.: 1 / Fragment: Death Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irak4 / Plasmid: pGEX6p1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8R4K2, EC: 2.7.1.37
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 25% PEG 3350, 10 mM MnCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B10.97888
SYNCHROTRONAPS 32-ID20.91947, 0.91919, 0.91270
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 29, 2004
MARRESEARCH2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.919471
30.919191
40.91271
ReflectionResolution: 1.7→18 Å / Num. obs: 13974

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.761 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22255 993 7.1 %RANDOM
Rwork0.17673 ---
obs0.17982 12981 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.62 Å2
2--0.68 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 1 145 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022842
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.991150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3035104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74424.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28615139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.909155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02630
X-RAY DIFFRACTIONr_nbd_refined0.280.2430
X-RAY DIFFRACTIONr_nbtor_refined0.3230.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.215
X-RAY DIFFRACTIONr_mcbond_it1.2451.5535
X-RAY DIFFRACTIONr_mcangle_it1.9682855
X-RAY DIFFRACTIONr_scbond_it3.353341
X-RAY DIFFRACTIONr_scangle_it5.1514.5295
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 71 -
Rwork0.231 916 -
obs--100 %

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