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- PDB-6bfn: Crystal structure of human IRAK1 -

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Basic information

Entry
Database: PDB / ID: 6bfn
TitleCrystal structure of human IRAK1
ComponentsInterleukin-1 receptor-associated kinase 1IRAK1
KeywordsTRANSFERASE / Interleukin-1 (IL-1) receptor-associated kinases
Function / homology
Function and homology information


: / regulation of cytokine-mediated signaling pathway / : / protein serine/threonine kinase activity => GO:0004674 / toll-like receptor 2 signaling pathway / : / : / MyD88 dependent cascade initiated on endosome / Transcriptional Regulation by MECP2 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation ...: / regulation of cytokine-mediated signaling pathway / : / protein serine/threonine kinase activity => GO:0004674 / toll-like receptor 2 signaling pathway / : / : / MyD88 dependent cascade initiated on endosome / Transcriptional Regulation by MECP2 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / toll-like receptor 9 signaling pathway / activation of NF-kappaB-inducing kinase activity / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / positive regulation of type I interferon production / JNK cascade / lipopolysaccharide-mediated signaling pathway / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / heat shock protein binding / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / viral process / NF-kB is activated and signals survival / lipid droplet / response to interleukin-1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / positive regulation of smooth muscle cell proliferation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of MAP kinase activity / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / PIP3 activates AKT signaling / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / kinase activity / cellular response to hypoxia / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / response to lipopolysaccharide / protein autophosphorylation / endosome membrane / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein heterodimerization activity / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 1, death domain / Interleukin-1 receptor-associated kinase 1 / Death domain / Death domain / Death-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Interleukin-1 receptor-associated kinase 1, death domain / Interleukin-1 receptor-associated kinase 1 / Death domain / Death domain / Death-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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
Chem-DL1 / Interleukin-1 receptor-associated kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å
AuthorsWang, L. / Qiao, Q. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI050872 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of human IRAK1.
Authors: Wang, L. / Qiao, Q. / Ferrao, R. / Shen, C. / Hatcher, J.M. / Buhrlage, S.J. / Gray, N.S. / Wu, H.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)76,3134
Polymers75,5552
Non-polymers7592
Water2,810156
1
A: Interleukin-1 receptor-associated kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1572
Polymers37,7771
Non-polymers3791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1572
Polymers37,7771
Non-polymers3791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.059, 88.059, 177.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Interleukin-1 receptor-associated kinase 1 / IRAK1 / IRAK-1


Mass: 37777.289 Da / Num. of mol.: 2 / Fragment: UNP residues 194-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK1, IRAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P51617, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-DL1 / N-[2-methoxy-4-(morpholin-4-yl)phenyl]-6-(1H-pyrazol-5-yl)pyridine-2-carboxamide


Mass: 379.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N5O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 20% PEG3350, 0.2 M calcium chloride, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2016
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.26→88.06 Å / Num. obs: 33471 / % possible obs: 100 % / Redundancy: 12.4 % / Net I/σ(I): 13.3
Reflection shellHighest resolution: 2.26 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.26→78.844 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.2269 1703 5.1 %
Rwork0.184 --
obs0.1861 33415 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→78.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 56 156 4907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054872
X-RAY DIFFRACTIONf_angle_d0.9166595
X-RAY DIFFRACTIONf_dihedral_angle_d14.4591843
X-RAY DIFFRACTIONf_chiral_restr0.033711
X-RAY DIFFRACTIONf_plane_restr0.004854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2601-2.32660.34971440.2642581X-RAY DIFFRACTION100
2.3266-2.40170.27181530.25122573X-RAY DIFFRACTION100
2.4017-2.48750.26641450.2252584X-RAY DIFFRACTION100
2.4875-2.58710.29811420.21252599X-RAY DIFFRACTION100
2.5871-2.70490.28681330.21152614X-RAY DIFFRACTION100
2.7049-2.84750.24251490.20142604X-RAY DIFFRACTION100
2.8475-3.02590.26121330.21212634X-RAY DIFFRACTION100
3.0259-3.25950.24581680.19692595X-RAY DIFFRACTION100
3.2595-3.58760.26591270.18322648X-RAY DIFFRACTION100
3.5876-4.10670.17891050.16282708X-RAY DIFFRACTION100
4.1067-5.17380.20311520.14972718X-RAY DIFFRACTION100
5.1738-78.89180.17111520.16952854X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -30.1412 Å / Origin y: 8.9839 Å / Origin z: 17.1108 Å
111213212223313233
T0.2213 Å20.0626 Å2-0.0292 Å2-0.2607 Å2-0.032 Å2--0.1936 Å2
L1.7116 °20.6386 °20.0171 °2-1.2915 °2-0.0576 °2--1.1195 °2
S-0.0119 Å °0.1399 Å °-0.0343 Å °-0.05 Å °0.0481 Å °0.0439 Å °-0.025 Å °-0.0568 Å °-0.0214 Å °
Refinement TLS groupSelection details: all

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