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- PDB-2o8y: Apo IRAK4 Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 2o8y
TitleApo IRAK4 Kinase Domain
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE / Protein kinase / immunodeficiency / inflammation
Function / homology
Function and homology information


IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding ...IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / interleukin-33-mediated signaling pathway / neutrophil migration / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / JNK cascade / positive regulation of smooth muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / Interleukin-1 signaling / cytokine-mediated signaling pathway / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / cell surface / extracellular space / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBoriack-Sjodin, P.A. / Mol, C.
CitationJournal: To be Published
Title: Crystal structures of the apo and inhibited IRAK4 kinase domain
Authors: Mol, C.D. / Arduini, R.M. / Baker, D.P. / Chien, E.Y. / Dougan, D.R. / Friedman, J. / Gibaja, V. / Hession, C.A. / Horne, A.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 receptor-associated kinase 4
B: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)67,9942
Polymers67,9942
Non-polymers00
Water1,06359
1
A: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9971
Polymers33,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9971
Polymers33,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.15, 118.64, 140.71
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Interleukin-1 receptor-associated kinase 4 / IRAK-4 / NY- REN-64 antigen


Mass: 33996.973 Da / Num. of mol.: 2 / Fragment: IRAK4 kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Plasmid: pFastBac HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL protein(14.5 mg/mL in 50 mM Tris-HCl pH 7.6, 250 mM NaCl, 250 mM TCEP, and 100 mM EDTA supplemented with 2 mM ADP and 4 mM MgCl2 prior to crystallization) and 1 uL of reservoir solution ...Details: 1 uL protein(14.5 mg/mL in 50 mM Tris-HCl pH 7.6, 250 mM NaCl, 250 mM TCEP, and 100 mM EDTA supplemented with 2 mM ADP and 4 mM MgCl2 prior to crystallization) and 1 uL of reservoir solution (100 mM HEPES pH 7.5, 20-25% PEG 3350, 200 mM ammonium sulfate), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29503 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.9 / % possible all: 85.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→35 Å / FOM work R set: 0.773 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1448 4.8 %random
Rwork0.244 ---
all0.246 29864 --
obs0.244 29503 98.8 %-
Displacement parametersBiso mean: 49.912 Å2
Baniso -1Baniso -2Baniso -3
1--8.422 Å20 Å20 Å2
2---1.508 Å20 Å2
3---9.931 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 59 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5151.5
X-RAY DIFFRACTIONc_scbond_it2.1542
X-RAY DIFFRACTIONc_mcangle_it2.5672
X-RAY DIFFRACTIONc_scangle_it3.1992.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.4-2.430.374470.33848895
2.43-2.460.353530.321913966
2.46-2.490.361450.304954999
2.49-2.530.398580.299641022
2.53-2.560.405470.31310051052
2.56-2.60.359570.2999631020
2.6-2.640.354560.299991055
2.64-2.680.379500.310151065
2.68-2.730.384500.2919961046
2.73-2.780.297510.28610051056
2.78-2.830.303490.26410141063
2.83-2.890.347580.2849961054
2.89-2.950.34470.24910041051
2.95-3.020.313500.24910311081
3.02-3.10.263560.2349961052
3.1-3.180.355450.2610051050
3.18-3.280.301550.26410101065
3.28-3.380.364430.26210141057
3.38-3.50.343650.2639981063
3.5-3.640.245630.22610101073
3.64-3.810.251520.22610251077
3.81-4.010.26520.21710041056
4.01-4.260.261510.20110341085
4.26-4.590.249370.21410301067
4.59-5.050.2540.210331087
5.05-5.780.254520.25110411093
5.78-7.270.31480.25310561104
7.27-350.249570.21510921149
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_tpo.param
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:water_rep.param

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