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- PDB-2oib: Crystal structure of IRAK4 kinase domain apo form -

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Basic information

Entry
Database: PDB / ID: 2oib
TitleCrystal structure of IRAK4 kinase domain apo form
ComponentsInterleukin-1 receptor-associated kinase 4
KeywordsTRANSFERASE / KINASE / HELIC C
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 / interleukin-1 receptor binding / neutrophil mediated immunity ...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 / interleukin-1 receptor binding / neutrophil mediated immunity / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / 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 / Interleukin-1 signaling / cytokine-mediated signaling pathway / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Interleukin-1 receptor-associated kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuglstatter, A. / Villasenor, A.G. / Browner, M.F.
CitationJournal: J.Immunol. / Year: 2007
Title: Cutting Edge: IL-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features and Multiple Conformations.
Authors: Kuglstatter, A. / Villasenor, A.G. / Shaw, D. / Lee, S.W. / Tsing, S. / Niu, L. / Song, K.W. / Barnett, J.W. / Browner, M.F.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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


Theoretical massNumber of molelcules
Total (without water)135,8254
Polymers135,8254
Non-polymers00
Water12,899716
1
A: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9561
Polymers33,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9561
Polymers33,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9561
Polymers33,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-1 receptor-associated kinase 4


Theoretical massNumber of molelcules
Total (without water)33,9561
Polymers33,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.066, 138.750, 87.942
Angle α, β, γ (deg.)90.00, 123.95, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE ASYMMETRIC UNIT CONTAINS 4 IRAK4 KINASE DOMAINS (CHAINS A-D), EACH OF WHICH REPRESENTS ONE BIOLOGICAL UNIT. CHAINS A AND C SHARE ONE PROTEIN CONFORMATION (HELIX C-OUT), CHAINS B AND D SHARE ANOTHER PROTEIN CONFORMATION (HELIX C-IN).

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Components

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


Mass: 33956.195 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAK4 / Production host: unidentified baculovirus
References: UniProt: Q9NWZ3, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.3M sodium malonate, 0.1M sodium acetate, 0.01M DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 87970 / % possible obs: 92.6 % / Observed criterion σ(F): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 9.3 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4252 / Rsym value: 0.51 / % possible all: 62.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWH

1uwh


Resolution: 2→48.56 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.107 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26981 4407 5 %RANDOM
Rwork0.2211 ---
obs0.22351 83552 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.108 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20.99 Å2
2---1.77 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9031 0 0 716 9747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229176
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.97512385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02151124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97725.477440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30315.0361688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2711540
X-RAY DIFFRACTIONr_chiral_restr0.0740.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026793
X-RAY DIFFRACTIONr_nbd_refined0.1840.24488
X-RAY DIFFRACTIONr_nbtor_refined0.2950.26350
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2727
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2120
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.220
X-RAY DIFFRACTIONr_mcbond_it0.5741.55843
X-RAY DIFFRACTIONr_mcangle_it1.00229116
X-RAY DIFFRACTIONr_scbond_it1.16133715
X-RAY DIFFRACTIONr_scangle_it1.8354.53269
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 194 -
Rwork0.294 3950 -
obs--59.16 %
Refinement TLS params.Method: refined / Origin x: 22.118 Å / Origin y: -16.5744 Å / Origin z: 17.7808 Å
111213212223313233
T-0.0581 Å2-0.0118 Å2-0.0189 Å2--0.0367 Å20.0076 Å2---0.0466 Å2
L0.3365 °2-0.0782 °2-0.2622 °2-0.2614 °20.0341 °2--0.4769 °2
S-0.0222 Å °-0.0314 Å °-0.0351 Å °-0.0066 Å °-0.0071 Å °-0.002 Å °-0.0321 Å °0.0537 Å °0.0294 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA162 - 4583 - 299
2X-RAY DIFFRACTION1BB164 - 4595 - 300
3X-RAY DIFFRACTION1CC161 - 4582 - 299
4X-RAY DIFFRACTION1DD162 - 4593 - 300

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