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- PDB-8wtf: The Crystal Structure of IRAK4 from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wtf
TitleThe Crystal Structure of IRAK4 from Biortus
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsSIGNALING PROTEIN / Kinase / Serine/threonine-protein kinase / Transferase / Immunity / Innate immunity / ATP-binding / Magnesium / Nucleotide-binding
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 / neutrophil migration / interleukin-33-mediated signaling pathway / 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 / neutrophil migration / interleukin-33-mediated signaling pathway / toll-like receptor 9 signaling pathway / neutrophil mediated immunity / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / extrinsic component of plasma membrane / toll-like receptor signaling pathway / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of smooth muscle cell proliferation / cytokine-mediated signaling pathway / Interleukin-1 signaling / PIP3 activates AKT signaling / kinase activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / endosome membrane / 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 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-8CG / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of IRAK4 from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
History
DepositionOct 18, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,9576
Polymers33,3131
Non-polymers6445
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.449, 93.061, 60.925
Angle α, β, γ (deg.)90.000, 99.146, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-692-

HOH

31A-744-

HOH

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Components

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


Mass: 33312.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-8CG / 1-{[(2S,3S,4S)-3-ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide


Mass: 361.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate,0.1M BisTris,5.5,25% w/vPEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.53 Å / Num. obs: 19106 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.515 / Num. unique obs: 1425

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.952 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2363 973 5.094 %
Rwork0.18 18129 -
all0.183 --
obs-19102 99.635 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.171 Å2
Baniso -1Baniso -2Baniso -3
1--1.004 Å2-0 Å2-1.101 Å2
2--2.932 Å20 Å2
3----1.497 Å2
Refinement stepCycle: LAST / Resolution: 2→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 43 165 2498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172269
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.6423209
X-RAY DIFFRACTIONr_angle_other_deg1.0751.5835248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82524.11118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57315435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.93159
X-RAY DIFFRACTIONr_chiral_restr0.0380.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.1540.2410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1530.21935
X-RAY DIFFRACTIONr_nbtor_refined0.1440.21168
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.2993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2130
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.29
X-RAY DIFFRACTIONr_nbd_other0.1130.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0860.210
X-RAY DIFFRACTIONr_mcbond_it7.3582.8061166
X-RAY DIFFRACTIONr_mcbond_other7.3572.8061165
X-RAY DIFFRACTIONr_mcangle_it8.424.1591455
X-RAY DIFFRACTIONr_mcangle_other8.4184.161456
X-RAY DIFFRACTIONr_scbond_it10.5453.6281214
X-RAY DIFFRACTIONr_scbond_other10.5283.621211
X-RAY DIFFRACTIONr_scangle_it13.0215.0871752
X-RAY DIFFRACTIONr_scangle_other13.0115.0771747
X-RAY DIFFRACTIONr_lrange_it14.48334.2962619
X-RAY DIFFRACTIONr_lrange_other14.51734.1292593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.274600.2341363X-RAY DIFFRACTION99.7896
2.052-2.1080.289600.2251307X-RAY DIFFRACTION99.8539
2.108-2.1690.224620.2121273X-RAY DIFFRACTION99.9251
2.169-2.2360.324700.1971214X-RAY DIFFRACTION99.6894
2.236-2.3090.252620.2021208X-RAY DIFFRACTION99.686
2.309-2.390.275520.1911144X-RAY DIFFRACTION99.8331
2.39-2.480.201640.1781113X-RAY DIFFRACTION99.9151
2.48-2.5810.225600.1781088X-RAY DIFFRACTION99.913
2.581-2.6960.232590.1781012X-RAY DIFFRACTION99.8136
2.696-2.8270.261580.17993X-RAY DIFFRACTION99.8101
2.827-2.9790.257640.182915X-RAY DIFFRACTION99.6945
2.979-3.160.22500.189885X-RAY DIFFRACTION99.7866
3.16-3.3770.249440.189839X-RAY DIFFRACTION99.6614
3.377-3.6470.253530.182754X-RAY DIFFRACTION99.262
3.647-3.9930.182430.157700X-RAY DIFFRACTION99.3316
3.993-4.4620.236360.135655X-RAY DIFFRACTION98.8555
4.462-5.1480.232310.153565X-RAY DIFFRACTION98.3498
5.148-6.2930.271200.179487X-RAY DIFFRACTION99.2172
6.293-8.8520.19140.175395X-RAY DIFFRACTION99.2718
8.852-46.530.11110.11219X-RAY DIFFRACTION98.2906

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