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- PDB-4loo: Structural basis of autoactivation of p38 alpha induced by TAB1 (... -

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Basic information

Entry
Database: PDB / ID: 4loo
TitleStructural basis of autoactivation of p38 alpha induced by TAB1 (Monoclinic crystal form)
Components
  • Mitogen-activated protein kinase 14
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / protein kinase / kinase-regulatory protein complex / MAPK / autoactivation / autophosphorylation
Function / homology
Function and homology information


IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling ...IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TNFR1-induced NF-kappa-B signaling pathway / cardiac septum development / TAK1-dependent IKK and NF-kappa-B activation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / p38MAPK events / Activation of the AP-1 family of transcription factors / Platelet sensitization by LDL / RHO GTPases Activate NADPH Oxidases / ERK/MAPK targets / myoblast differentiation involved in skeletal muscle regeneration / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / ADP signalling through P2Y purinoceptor 1 / Regulation of TP53 Activity through Phosphorylation / Myogenesis / positive regulation of cGAS/STING signaling pathway / Ub-specific processing proteases / VEGFA-VEGFR2 Pathway / coronary vasculature development / kinase activator activity / non-canonical NF-kappaB signal transduction / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / aorta development / positive regulation of myoblast fusion / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / response to dietary excess / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / protein serine/threonine phosphatase activity / regulation of ossification / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / heart morphogenesis / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / striated muscle cell differentiation / response to muscle stretch / Neutrophil degranulation / positive regulation of interleukin-12 production / transforming growth factor beta receptor signaling pathway / lung development / osteoclast differentiation / positive regulation of erythrocyte differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / protein serine/threonine kinase activator activity / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / positive regulation of D-glucose import / stem cell differentiation / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / cellular response to virus / positive regulation of protein import into nucleus / glucose metabolic process / cell morphogenesis / positive regulation of reactive oxygen species metabolic process / spindle pole / osteoblast differentiation / cellular response to tumor necrosis factor / kinase activity / MAPK cascade / cellular response to lipopolysaccharide / angiogenesis / protein phosphatase binding / response to lipopolysaccharide / molecular adaptor activity / in utero embryonic development / transcription by RNA polymerase II / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction
Similarity search - Function
Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-SB4 / Mitogen-activated protein kinase 14 / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChaikuad, A. / DeNicola, G.F. / Krojer, T. / Allerston, C.K. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Marber, M.S. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Mechanism and consequence of the autoactivation of p38 alpha mitogen-activated protein kinase promoted by TAB1.
Authors: De Nicola, G.F. / Martin, E.D. / Chaikuad, A. / Bassi, R. / Clark, J. / Martino, L. / Verma, S. / Sicard, P. / Tata, R. / Atkinson, R.A. / Knapp, S. / Conte, M.R. / Marber, M.S.
History
DepositionJul 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8363
Polymers44,4982
Non-polymers3381
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-24 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.340, 73.580, 59.190
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAP kinase 14 / MAPK 14 / CRK1 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha


Mass: 41395.211 Da / Num. of mol.: 1 / Fragment: kinase domain (1-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MAPK14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli (E. coli)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Protein/peptide TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 3102.515 Da / Num. of mol.: 1 / Fragment: residues 384-412 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CF89
#3: Chemical ChemComp-SB4 / 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE / SB220025


Mass: 338.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19FN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% medium-molecular weight PEG Smears, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2012
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→59.18 Å / Num. all: 27022 / Num. obs: 27019 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2 / Num. unique all: 3898 / % possible all: 98.7

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QUE

3que


Resolution: 1.95→46.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.841 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.192 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25024 1354 5 %RANDOM
Rwork0.19754 ---
all0.241 27019 --
obs0.20033 25658 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.518 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å2-0.29 Å2
2---1.38 Å20 Å2
3----1.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 1.95→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 25 171 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023036
X-RAY DIFFRACTIONr_bond_other_d0.0020.022005
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9734141
X-RAY DIFFRACTIONr_angle_other_deg1.0513.0044911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62324.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811515
X-RAY DIFFRACTIONr_chiral_restr0.090.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 104 -
Rwork0.305 1809 -
obs--98.46 %
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)
11.2419-0.8390.51731.7991.03161.8368-0.142-0.00690.22550.02960.1993-0.2728-0.00430.1975-0.05720.2565-0.0255-0.00310.2389-0.01650.267421.9483-20.92639.8005
21.0265-0.1862-0.0511.517-0.86842.8410.04320.10860.159-0.0748-0.02060.0057-0.1272-0.3638-0.02260.24260.017-0.00170.27370.00790.22268.1352-15.101516.2511
30.8652-0.2910.35670.83070.43673.0486-0.04950.0474-0.01060.0334-0.0050.12690.0374-0.42360.05450.1912-0.0595-0.01270.2624-0.01890.20213.9602-21.821623.8697
45.2512-9.118-0.008418.1639-2.09651.92350.2580.96680.2136-0.5898-0.864-1.00670.2806-0.67820.6060.69980.15770.0030.4881-0.18970.18812.7846-26.1399-0.3804
50.30812.67572.10324.630320.198217.10.07650.06030.04552.3091.0445-0.5562.16191.4346-1.1210.41490.3305-0.29210.5723-0.4010.685121.6594-34.605514.2587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 109
2X-RAY DIFFRACTION2A110 - 264
3X-RAY DIFFRACTION3A265 - 353
4X-RAY DIFFRACTION4B384 - 394
5X-RAY DIFFRACTION5B395 - 411

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