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- PDB-4u9a: Sulphur Anomalous Crystal Structure of Asymmetric IRAK4 Dimer -

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Basic information

Entry
Database: PDB / ID: 4u9a
TitleSulphur Anomalous Crystal Structure of Asymmetric IRAK4 Dimer
ComponentsInterleukin-1 receptor-associated kinase 4IRAK4
KeywordsTRANSFERASE / Kinase / Sulphur Anomalous / Autophosphorylation
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 / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / extrinsic component of plasma membrane / JNK cascade / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of smooth muscle cell proliferation / Interleukin-1 signaling / cytokine-mediated signaling pathway / PIP3 activates AKT signaling / kinase activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / endosome membrane / 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 / cytosol / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain ...Interleukin-1 receptor-associated kinase 4 / IRAK4, Death domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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: 2.8 Å
AuthorsFerrao, R. / Liu, Q. / 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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-48 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.495, 87.495, 424.039
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Interleukin-1 receptor-associated kinase 4 / IRAK4 / 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 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mg/ml IRAK4 mixed with staurosproine at a 2:1 molar excess. Protein solution mixed 1:1 with 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: X4A / Wavelength: 2.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07 Å / Relative weight: 1
ReflectionResolution: 2.8→38.88 Å / Num. obs: 43351 / % possible obs: 97.3 % / Redundancy: 212.6 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 45.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.879 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 3574 8.24 %
Rwork0.1802 --
obs0.185 43351 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→38.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 85 0 4349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084430
X-RAY DIFFRACTIONf_angle_d1.1475994
X-RAY DIFFRACTIONf_dihedral_angle_d14.9541624
X-RAY DIFFRACTIONf_chiral_restr0.04671
X-RAY DIFFRACTIONf_plane_restr0.006753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83680.58841040.4691177X-RAY DIFFRACTION75
2.8368-2.87570.4831080.37821269X-RAY DIFFRACTION81
2.8757-2.91680.38821160.34331311X-RAY DIFFRACTION80
2.9168-2.96030.36171340.2951438X-RAY DIFFRACTION93
2.9603-3.00650.3441370.26911526X-RAY DIFFRACTION95
3.0065-3.05580.33841360.24531531X-RAY DIFFRACTION99
3.0558-3.10850.33911440.23081584X-RAY DIFFRACTION100
3.1085-3.1650.31111400.22251571X-RAY DIFFRACTION100
3.165-3.22580.25491460.2091589X-RAY DIFFRACTION100
3.2258-3.29160.26451430.22281551X-RAY DIFFRACTION100
3.2916-3.36320.32421390.22131614X-RAY DIFFRACTION100
3.3632-3.44130.33121330.24071536X-RAY DIFFRACTION100
3.4413-3.52730.2421440.21241594X-RAY DIFFRACTION100
3.5273-3.62270.25511420.19061579X-RAY DIFFRACTION100
3.6227-3.72920.21221380.18491538X-RAY DIFFRACTION100
3.7292-3.84940.2141460.17311582X-RAY DIFFRACTION100
3.8494-3.98690.18911490.15771622X-RAY DIFFRACTION100
3.9869-4.14630.21751400.14731537X-RAY DIFFRACTION100
4.1463-4.33480.19971450.13391593X-RAY DIFFRACTION100
4.3348-4.5630.16881440.141560X-RAY DIFFRACTION100
4.563-4.84840.18811420.12971584X-RAY DIFFRACTION100
4.8484-5.2220.20631460.13671564X-RAY DIFFRACTION100
5.222-5.7460.23671380.1651579X-RAY DIFFRACTION100
5.746-6.57390.31321390.18141587X-RAY DIFFRACTION100
6.5739-8.26940.23011390.17951577X-RAY DIFFRACTION100
8.2694-38.8830.22751420.18671584X-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)
11.5086-0.74-0.62442.22940.34691.67820.0681-0.4421-1.0169-0.5571-0.5881-0.95581.36761.55340.34091.30520.64140.04111.56120.50211.42335.667816.116926.1136
22.10490.3161-0.1394.052-0.56831.61790.07-1.0599-0.3077-0.323-0.1955-0.55720.17981.08730.11330.47630.1087-0.03691.40760.17110.79343.425731.33523.5261
34.4686-0.4406-0.14423.6541-0.27783.96560.5685-0.22430.4968-0.7808-0.5106-0.1363-0.52840.4987-0.07090.4857-0.01680.14190.980.07460.6934-1.40744.635714.2956
43.9445-2.1873-0.95013.88612.38916.4866-0.74210.1127-0.4557-0.18170.26120.69712.8154-0.53940.43631.3074-0.3440.01760.95260.16550.95147.419417.6622-30.2908
51.4163-0.7751-0.80353.66930.47941.9358-0.44640.39130.08-0.49650.36830.90130.2603-0.8340.08750.532-0.19040.04581.27480.09280.9421-0.926426.154-28.4643
64.0701-0.6753-0.18233.3402-0.55394.09790.1011-0.46810.03070.42890.07790.3916-0.6944-0.5286-0.15120.47910.17750.20490.95770.07410.67759.122343.8771-14.0452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 166 through 247 )
2X-RAY DIFFRACTION2chain 'B' and (resid 248 through 350 )
3X-RAY DIFFRACTION3chain 'B' and (resid 351 through 458 )
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 269 )
6X-RAY DIFFRACTION6chain 'A' and (resid 270 through 458 )

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