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- PDB-4u97: Crystal Structure of Asymmetric IRAK4 Dimer -

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Basic information

Entry
Database: PDB / ID: 4u97
TitleCrystal Structure of Asymmetric IRAK4 Dimer
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE / Kinase / Autophosphorylation / Dimer
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
STAUROSPORINE / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFerrao, R. / Wu, H.
CitationJournal: Mol.Cell / Year: 2014
Title: IRAK4 Dimerization and trans-Autophosphorylation Are Induced by Myddosome Assembly.
Authors: Ferrao, R. / Zhou, H. / Shan, Y. / Liu, Q. / Li, Q. / Shaw, D.E. / Li, X. / Wu, H.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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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
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8627
Polymers69,6412
Non-polymers1,2215
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-47 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.580, 87.580, 421.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

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


Mass: 34820.469 Da / Num. of mol.: 2 / Mutation: D311N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Set up at 10 mg/mL with staurosporine at a 2:1 molar ratio. Mixed with equal volumes 1.6-1.9 M ammonium sulfate, 100 mM Hepes-NaOH at pH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.65→41.81 Å / Num. obs: 29127 / % possible obs: 100 % / Redundancy: 83.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 37.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→41.807 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2000 6.87 %
Rwork0.2026 --
obs0.2058 29121 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→41.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 85 97 4446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084430
X-RAY DIFFRACTIONf_angle_d1.1115994
X-RAY DIFFRACTIONf_dihedral_angle_d14.7121624
X-RAY DIFFRACTIONf_chiral_restr0.039671
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71630.31731380.27071864X-RAY DIFFRACTION100
2.7163-2.78970.32751380.24381872X-RAY DIFFRACTION100
2.7897-2.87180.3241390.24161893X-RAY DIFFRACTION100
2.8718-2.96440.28111400.25061888X-RAY DIFFRACTION100
2.9644-3.07040.28531380.22541885X-RAY DIFFRACTION100
3.0704-3.19320.3111410.23271911X-RAY DIFFRACTION100
3.1932-3.33850.27421410.23281903X-RAY DIFFRACTION100
3.3385-3.51440.28981410.21041925X-RAY DIFFRACTION100
3.5144-3.73450.22451420.19351913X-RAY DIFFRACTION100
3.7345-4.02260.20551420.1731941X-RAY DIFFRACTION100
4.0226-4.4270.21151440.15821945X-RAY DIFFRACTION100
4.427-5.06670.20111460.16141984X-RAY DIFFRACTION100
5.0667-6.37990.27011490.2032011X-RAY DIFFRACTION100
6.3799-41.81240.24281610.21712186X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2449-0.30810.30420.1504-0.61132.7248-0.33110.0619-1.0817-0.3603-0.1654-0.62511.54830.54170.16641.310.46220.00941.020.19430.91888.505210.980626.4227
20.94-0.0474-0.27732.9489-0.42811.71910.07-0.4065-0.5956-0.2339-0.0787-0.23280.8090.71630.76890.96730.5081-0.04110.91860.31760.882690.895514.953727.5354
31.17220.3764-0.61831.17680.17741.93440.1747-0.3063-0.538-0.178-0.3252-1.13830.5930.89290.51060.56450.35550.05271.48880.45361.1601102.232725.316724.4977
42.64670.2392-0.30022.9210.2322.47490.1851-0.4209-0.236-0.368-0.2843-0.79980.38871.0585-0.02860.1650.12680.01960.94970.17460.475190.986631.553923.4117
54.6496-0.5063-1.36641.80080.3510.81260.26020.6764-0.144-0.5445-0.3895-0.26580.24240.4452-0.14570.25430.14150.12950.74730.12460.375887.610838.226510.3592
67.9392-1.0029-0.74626.7848-0.7034.031.09980.62911.4422-0.8642-0.4760.0161-1.03390.3237-0.27780.48830.13290.19140.73630.11960.534478.57249.72729.1607
75.67770.9777-0.10912.52710.1561.34020.5809-0.53240.8506-0.1393-0.3391-0.5654-0.89840.5427-0.20170.3507-0.11340.18590.72270.01760.526488.028248.680419.9053
85.4888-4.0519-3.39153.18223.63668.91070.43720.1035-0.76130.1239-0.74212.84642.5424-1.45480.0531.3495-0.4301-0.45170.86150.0311.259688.625615.7454-35.5114
95.16442.80123.40519.31281.9687.0921-0.38520.0084-1.5784-0.28990.4865-0.30753.2274-0.0601-0.24951.13230.00880.05540.5164-0.07310.6187100.624814.9463-28.8418
106.4653-5.9848-5.94965.5765.5085.4952-1.1153-0.9434-1.01211.14290.28020.48271.9912-0.49390.91930.7071-0.06040.06150.80660.13120.640799.692221.9053-24.7926
116.0063-1.6979-1.02923.8574-0.43053.4349-0.16680.41590.4239-1.05610.77281.48692.0146-1.091-0.35830.6654-0.3084-0.08110.68850.1240.591792.703121.9118-31.4286
120.1136-0.7210.10025.72541.67744.50450.15450.1149-0.29420.3297-0.10192.30.7246-1.7735-0.28560.4881-0.05620.01311.69430.12521.106180.86629.5957-24.6522
132.7691-0.4437-0.89762.4848-0.24742.4751-0.03920.1504-0.1206-0.15050.24810.50980.0356-1.1099-0.11110.13170.09940.08290.86270.11780.36693.860637.1519-24.8345
140.9617-0.8696-0.75511.58481.37711.1987-0.0341-0.366-1.00160.57020.5160.49970.5173-0.7458-0.65090.45350.05840.12211.09930.22410.841592.218631.4359-7.963
154.4286-0.1651-1.75262.0469-0.8663.23490.219-0.62820.37460.5685-0.03330.1009-1.1294-0.4007-0.52740.38050.2150.2520.85490.00130.340198.366647.3032-10.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 166 through 197 )
2X-RAY DIFFRACTION2chain 'B' and (resid 198 through 226 )
3X-RAY DIFFRACTION3chain 'B' and (resid 227 through 247 )
4X-RAY DIFFRACTION4chain 'B' and (resid 248 through 350 )
5X-RAY DIFFRACTION5chain 'B' and (resid 351 through 395 )
6X-RAY DIFFRACTION6chain 'B' and (resid 396 through 413 )
7X-RAY DIFFRACTION7chain 'B' and (resid 414 through 458 )
8X-RAY DIFFRACTION8chain 'A' and (resid 166 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 184 )
10X-RAY DIFFRACTION10chain 'A' and (resid 185 through 197 )
11X-RAY DIFFRACTION11chain 'A' and (resid 198 through 217 )
12X-RAY DIFFRACTION12chain 'A' and (resid 226 through 247 )
13X-RAY DIFFRACTION13chain 'A' and (resid 248 through 324 )
14X-RAY DIFFRACTION14chain 'A' and (resid 325 through 354 )
15X-RAY DIFFRACTION15chain 'A' and (resid 355 through 458 )

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