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- PDB-6ziw: The IRAK3 Pseudokinase Domain Bound To ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 6ziw
TitleThe IRAK3 Pseudokinase Domain Bound To ATPgammaS
ComponentsInterleukin-1 receptor-associated kinase 3
KeywordsSIGNALING PROTEIN / Kinase Pseudokinase Nucleotide binding
Function / homology
Function and homology information


positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of protein-containing complex disassembly / negative regulation of macrophage cytokine production / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / interleukin-1-mediated signaling pathway ...positive regulation of macrophage tolerance induction / regulation of protein-containing complex disassembly / negative regulation of cytokine-mediated signaling pathway / negative regulation of protein-containing complex disassembly / negative regulation of macrophage cytokine production / response to peptidoglycan / Toll signaling pathway / negative regulation of toll-like receptor signaling pathway / negative regulation of interleukin-12 production / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of NF-kappaB transcription factor activity / response to exogenous dsRNA / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of MAP kinase activity / negative regulation of innate immune response / response to interleukin-1 / positive regulation of cytokine production / response to virus / negative regulation of protein catabolic process / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / response to lipopolysaccharide / intracellular signal transduction / protein heterodimerization activity / protein phosphorylation / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-1 receptor-associated kinase 3, pseudokinase domain / IRAK3, death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Interleukin-1 receptor-associated kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Kraemer, A. / Knapp, S.
CitationJournal: To Be Published
Title: The IRAK3 Pseudokinase Domain Bound To ATPgammaS
Authors: Mathea, S. / Chatterjee, D. / Preuss, F. / Kraemer, A. / Knapp, S.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Interleukin-1 receptor-associated kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1934
Polymers36,4771
Non-polymers7153
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-38 kcal/mol
Surface area12440 Å2
Unit cell
Length a, b, c (Å)190.450, 190.450, 190.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11I-661-

HOH

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Components

#1: Protein Interleukin-1 receptor-associated kinase 3 / IRAK-3 / IL-1 receptor-associated kinase M / IRAK-M


Mass: 36477.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y616, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.95 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M lithium sulphate 0.5 M ammonium sulphate 0.1 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.18→44.89 Å / Num. obs: 30909 / % possible obs: 97.38 % / Redundancy: 8 % / Biso Wilson estimate: 47.37 Å2 / CC1/2: 1 / Net I/σ(I): 25.6
Reflection shellResolution: 2.18→2.258 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2438 / CC1/2: 0.944 / % possible all: 80.65

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless7.0.078data scaling
PHASER7.0.078phasing
REFMAC7.0.078refinement
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BFN

6bfn


Resolution: 2.18→44.89 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 32.8465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 1486 4.94 %
Rwork0.216 28620 -
obs0.2177 30106 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.03 Å2
Refinement stepCycle: LAST / Resolution: 2.18→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 41 62 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862154
X-RAY DIFFRACTIONf_angle_d0.9842930
X-RAY DIFFRACTIONf_chiral_restr0.0549337
X-RAY DIFFRACTIONf_plane_restr0.0056374
X-RAY DIFFRACTIONf_dihedral_angle_d15.7305309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.250.59471320.54932193X-RAY DIFFRACTION84.76
2.25-2.330.3431260.33112260X-RAY DIFFRACTION86.73
2.33-2.420.28041290.2662643X-RAY DIFFRACTION99.86
2.42-2.530.26461370.22972631X-RAY DIFFRACTION100
2.53-2.670.24791340.22142641X-RAY DIFFRACTION100
2.67-2.830.21981270.21932667X-RAY DIFFRACTION100
2.84-3.050.25211550.2172636X-RAY DIFFRACTION99.96
3.05-3.360.28591210.21972678X-RAY DIFFRACTION100
3.36-3.850.2521440.20392673X-RAY DIFFRACTION99.86
3.85-4.840.20881500.17172719X-RAY DIFFRACTION100
4.85-44.890.23441310.21422879X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: 16.5882825135 Å / Origin y: -24.2808228026 Å / Origin z: -6.78318899894 Å
111213212223313233
T0.412298235788 Å20.108833200457 Å2-0.0789606178683 Å2-0.409717309642 Å20.055208249687 Å2--0.46497715051 Å2
L1.001168902 °2-0.527303462456 °2-0.68201398883 °2-1.5724061884 °20.846784115233 °2--3.20528750817 °2
S0.126465359992 Å °-0.128038853161 Å °0.105658606914 Å °0.264441849318 Å °0.281353770896 Å °-0.258186082952 Å °0.320645970599 Å °0.345706417717 Å °-0.327391988405 Å °
Refinement TLS groupSelection details: all

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