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- PDB-6mom: Crystal structure of human Interleukin-1 receptor associated Kina... -

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Basic information

Entry
Database: PDB / ID: 6mom
TitleCrystal structure of human Interleukin-1 receptor associated Kinase 4 (IRAK 4, CID 100300) in complex with compound NCC00371481 (BSI 107591)
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Interleukin-1 receptor associated Kinase 4 / CID 100300 / NCC00371481 / BSI 107591 / Beryllium / TRANSFERASE-TRANSFERASE INHIBITOR complex
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:MAL(TIRAP) cascade initiated on plasma membrane / MyD88-dependent toll-like receptor signaling pathway / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / JNK cascade / positive regulation of smooth muscle cell proliferation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / cytokine-mediated signaling pathway / Interleukin-1 signaling / kinase activity / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / cytoplasm / cytosol
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 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. ...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 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JX4 / Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Starczynowski, D. / Hoyt, S. / Tawa, G. / Thomas, C.
CitationJournal: Sci Transl Med / Year: 2019
Title: Overcoming adaptive therapy resistance in AML by targeting immune response pathways.
Authors: Melgar, K. / Walker, M.M. / Jones, L.M. / Bolanos, L.C. / Hueneman, K. / Wunderlich, M. / Jiang, J.K. / Wilson, K.M. / Zhang, X. / Sutter, P. / Wang, A. / Xu, X. / Choi, K. / Tawa, G. / ...Authors: Melgar, K. / Walker, M.M. / Jones, L.M. / Bolanos, L.C. / Hueneman, K. / Wunderlich, M. / Jiang, J.K. / Wilson, K.M. / Zhang, X. / Sutter, P. / Wang, A. / Xu, X. / Choi, K. / Tawa, G. / Lorimer, D. / Abendroth, J. / O'Brien, E. / Hoyt, S.B. / Berman, E. / Famulare, C.A. / Mulloy, J.C. / Levine, R.L. / Perentesis, J.P. / Thomas, C.J. / Starczynowski, D.T.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Interleukin-1 receptor-associated kinase 4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,08310
Polymers136,4014
Non-polymers1,6826
Water17,691982
1
A: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4902
Polymers34,1001
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5523
Polymers34,1001
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4902
Polymers34,1001
Non-polymers3891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-1 receptor-associated kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5523
Polymers34,1001
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.290, 141.910, 87.890
Angle α, β, γ (deg.)90.000, 126.220, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 164 through 166 or resid 168...
21(chain B and (resid 164 through 166 or resid 168...
31(chain C and ((resid 164 and (name N or name...
41(chain D and ((resid 164 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHISHIS(chain A and (resid 164 through 166 or resid 168...AA164 - 1667 - 9
12PHEPHEPHEPHE(chain A and (resid 164 through 166 or resid 168...AA168 - 17011 - 13
13ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
14ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
15ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
16ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
17ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
18ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
19ARGARGJX4JX4(chain A and (resid 164 through 166 or resid 168...AA - E164 - 5007
21ARGARGHISHIS(chain B and (resid 164 through 166 or resid 168...BB164 - 1667 - 9
22PHEPHEPHEPHE(chain B and (resid 164 through 166 or resid 168...BB168 - 17011 - 13
23TYRTYRTYRTYR(chain B and (resid 164 through 166 or resid 168...BB17114
24ARGARGALAALA(chain B and (resid 164 through 166 or resid 168...BB164 - 4597 - 302
25ARGARGALAALA(chain B and (resid 164 through 166 or resid 168...BB164 - 4597 - 302
26ARGARGALAALA(chain B and (resid 164 through 166 or resid 168...BB164 - 4597 - 302
27ARGARGALAALA(chain B and (resid 164 through 166 or resid 168...BB164 - 4597 - 302
31ARGARGARGARG(chain C and ((resid 164 and (name N or name...CC1647
32THRTHRSERSER(chain C and ((resid 164 and (name N or name...CC163 - 4606 - 303
33THRTHRSERSER(chain C and ((resid 164 and (name N or name...CC163 - 4606 - 303
34THRTHRSERSER(chain C and ((resid 164 and (name N or name...CC163 - 4606 - 303
35THRTHRSERSER(chain C and ((resid 164 and (name N or name...CC163 - 4606 - 303
41ARGARGARGARG(chain D and ((resid 164 and (name N or name...DD1647
42ARGARGALAALA(chain D and ((resid 164 and (name N or name...DD164 - 4597 - 302
43ARGARGALAALA(chain D and ((resid 164 and (name N or name...DD164 - 4597 - 302
44ARGARGALAALA(chain D and ((resid 164 and (name N or name...DD164 - 4597 - 302
45ARGARGALAALA(chain D and ((resid 164 and (name N or name...DD164 - 4597 - 302

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Components

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


Mass: 34100.320 Da / Num. of mol.: 4 / Fragment: UNP residues 160-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Plasmid: CID100300 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-JX4 / 6-[7-methoxy-6-(1-methyl-1H-pyrazol-4-yl)imidazo[1,2-a]pyridin-3-yl]-N-[(3R)-pyrrolidin-3-yl]pyridin-2-amine


Mass: 389.454 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 9.5 mg/ml IRAK4 (CID100300, Batch BOS047020B) in 20 mM Tris-HCl, pH 8.0, 1 mM DTT, with 1 mM BSI107659 (NCGC00371481) in DMSO, crystallization condition: Microlytic screen MCSG1, E10: 0.2 M ...Details: 9.5 mg/ml IRAK4 (CID100300, Batch BOS047020B) in 20 mM Tris-HCl, pH 8.0, 1 mM DTT, with 1 mM BSI107659 (NCGC00371481) in DMSO, crystallization condition: Microlytic screen MCSG1, E10: 0.2 M ammonium tartrate dibasic, 20% PEG3350, cryoprotectant: 20% ethylene glycol with 1 mM compound, tray 286446 e10, puck: xvc2-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 21, 2016 / Details: RIGAKU VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→45.729 Å / Num. obs: 79032 / % possible obs: 98.9 % / Redundancy: 7.47 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Χ2: 0.992 / Net I/σ(I): 15.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.5680.4335.156940.9230.4796.2
2.15-2.217.4530.3826.2556240.9490.4198.5
2.21-2.287.4670.3516.7154830.9610.37798.7
2.28-2.357.4490.3027.4853500.9760.32498.8
2.35-2.427.4850.2678.3952310.9790.28798.9
2.42-2.517.4810.2169.850150.9860.23299.2
2.51-2.67.5190.2119.949140.9870.22799.1
2.6-2.717.5550.1711.4146440.9920.18299.3
2.71-2.837.590.14312.645460.9940.15399.5
2.83-2.977.5980.12114.0842880.9960.1399.6
2.97-3.137.6180.09716.3941000.9970.10499.6
3.13-3.327.6280.08419.0939020.9980.0999.4
3.32-3.557.6420.06525.6336720.9980.06999.5
3.55-3.837.6070.05531.8434060.9980.05999.5
3.83-4.27.6270.04735.6331380.9990.05199.3
4.2-4.77.4470.04536.828200.9990.04999.3
4.7-5.427.5880.04733.8525150.9990.05199.4
5.42-6.647.6470.05528.921260.9990.05999
6.64-9.397.6260.0433.8316480.9990.04399
9.39-45.7297.3090.02843.839160.9990.0396.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NRU as per Morda

2nru


Resolution: 2.1→45.729 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2041 2.58 %0
Rwork0.1672 ---
obs0.1682 78992 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.61 Å2 / Biso mean: 32.1855 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 2.1→45.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8976 0 124 1011 10111
Biso mean--20.38 37.24 -
Num. residues----1166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079521
X-RAY DIFFRACTIONf_angle_d0.92112957
X-RAY DIFFRACTIONf_chiral_restr0.0581464
X-RAY DIFFRACTIONf_plane_restr0.0061668
X-RAY DIFFRACTIONf_dihedral_angle_d16.1515814
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4558X-RAY DIFFRACTION9.601TORSIONAL
12B4558X-RAY DIFFRACTION9.601TORSIONAL
13C4558X-RAY DIFFRACTION9.601TORSIONAL
14D4558X-RAY DIFFRACTION9.601TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.26821290.2014962509196
2.1489-2.20260.24061290.18885096522599
2.2026-2.26210.2631440.18875081522599
2.2621-2.32870.23061470.18115047519499
2.3287-2.40390.20881470.1775101524899
2.4039-2.48980.211440.17145136528099
2.4898-2.58950.24741520.181851065258100
2.5895-2.70730.23231380.180251315269100
2.7073-2.850.24721250.183151685293100
2.85-3.02850.22431270.171651805307100
3.0285-3.26230.20091370.171851655302100
3.2623-3.59050.21361100.155251835293100
3.5905-4.10980.18031450.139751765321100
4.1098-5.17670.15121310.141451895320100
5.1767-45.73940.19171360.18195230536699
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)
14.889-0.13231.69793.64710.29713.8498-0.24540.24440.2468-0.33620.19780.1324-0.281-0.0710.01730.2556-0.0547-0.02840.1964-0.00930.140725.6839.5187-18.8638
21.92590.9078-0.13752.3237-0.34561.9181-0.02220.07010.0355-0.04820.0601-0.1664-0.2670.1726-0.03330.1776-0.02230.00570.14550.00910.120439.557319.4755-1.1777
32.5438-0.69330.90710.9042-0.77842.002-0.0604-0.29180.05950.21660.08380.0469-0.1192-0.0629-0.02420.17360.0030.01840.1107-0.01910.148622.01289.868435.6094
42.0046-0.7332-0.26112.89160.66072.9609-0.00290.01450.0674-0.02180.04520.2609-0.4792-0.358-0.01060.22050.07070.01340.18720.01680.1949.588322.896522.6402
55.2514-0.81630.54750.60210.16691.4177-0.04330.0049-0.22650.0341-0.01360.1758-0.1252-0.33510.05770.17470.0091-0.01320.19640.01820.2228-8.5616-9.687732.3099
62.08820.4925-0.34312.8064-0.78912.4467-0.0453-0.1324-0.17510.20780.0089-0.00060.02630.03390.03560.1199-0.0113-0.00270.14460.02550.13629.6958-20.799542.1993
74.6250.3155-0.12083.52790.43374.8775-0.0608-0.2241-0.18660.15710.0825-0.04320.14260.1697-0.01140.11840.0173-0.0420.1461-0.00670.124645.527-8.740320.4668
82.01260.2457-0.09551.65990.47611.271-0.13110.2815-0.2515-0.19180.0905-0.04760.11860.00540.03790.1724-0.01470.0080.1596-0.02840.125928.4748-17.57746.3805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 258 )A164 - 258
2X-RAY DIFFRACTION2chain 'A' and (resid 259 through 460 )A259 - 460
3X-RAY DIFFRACTION3chain 'B' and (resid 164 through 324 )B164 - 324
4X-RAY DIFFRACTION4chain 'B' and (resid 325 through 459 )B325 - 459
5X-RAY DIFFRACTION5chain 'C' and (resid 163 through 284 )C163 - 284
6X-RAY DIFFRACTION6chain 'C' and (resid 285 through 460 )C285 - 460
7X-RAY DIFFRACTION7chain 'D' and (resid 164 through 222 )D164 - 222
8X-RAY DIFFRACTION8chain 'D' and (resid 223 through 459 )D223 - 459

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