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- PDB-5o90: Crystal structure of a P38alpha T185G mutant in complex with TAB1... -

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Basic information

Entry
Database: PDB / ID: 5o90
TitleCrystal structure of a P38alpha T185G mutant in complex with TAB1 peptide.
Components
  • Mitogen-activated protein kinase 14
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsTRANSFERASE / MAPK14 TRANSFERASE TAB1
Function / homology
Function and homology information


cardiac septum development / 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 ...cardiac septum development / 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 / VEGFA-VEGFR2 Pathway / coronary vasculature development / non-canonical NF-kappaB signal transduction / aorta development / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / cartilage condensation / cellular response to UV-B / protein serine/threonine phosphatase activity / 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 / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / JUN kinase activity / mitogen-activated protein kinase / chondrocyte differentiation / negative regulation of hippo signaling / positive regulation of myoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / skeletal muscle tissue development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / Neutrophil degranulation / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / transforming growth factor beta receptor signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / protein serine/threonine kinase activator activity / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / cellular response to ionizing radiation / positive regulation of D-glucose import / activated TAK1 mediates p38 MAPK activation / stem cell differentiation / response to insulin / placenta development / lung development / negative regulation of canonical Wnt signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / cell morphogenesis / bone development / cellular response to virus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / positive regulation of protein import into nucleus / Interleukin-1 signaling / glucose metabolic process / spindle pole / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / kinase activity / MAPK cascade / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / angiogenesis / molecular adaptor activity / response to lipopolysaccharide / in utero embryonic development / transcription by RNA polymerase II / protein kinase activity
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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsNichols, C.E. / De Nicola, G.F. / Thapa, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BHFBHF - FS/14/29/30896 - DE NICOLA United Kingdom
CitationJournal: Mol. Cell. Biol. / Year: 2018
Title: TAB1-Induced Autoactivation of p38 alpha Mitogen-Activated Protein Kinase Is Crucially Dependent on Threonine 185.
Authors: Thapa, D. / Nichols, C. / Bassi, R. / Martin, E.D. / Verma, S. / Conte, M.R. / De Santis, V. / De Nicola, G.F. / Marber, M.S.
History
DepositionJun 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jan 17, 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
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)44,7353
Polymers44,3972
Non-polymers3381
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.920, 73.580, 58.970
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41294.109 Da / Num. of mol.: 1 / Mutation: T185G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2
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: UNP residues 386-414 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15750
#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.: 8 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350 0.2M Na/K Tartrate 0.1M pH7.0 Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→58.96 Å / Num. obs: 18410 / % possible obs: 99.5 % / Redundancy: 9.4 % / Biso Wilson estimate: 67.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1340 / CC1/2: 0.651 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOO

4loo


Resolution: 2.49→58.959 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 39.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 617 4.47 %Random Selection
Rwork0.249 ---
obs0.2502 13808 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→58.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 25 8 2599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012662
X-RAY DIFFRACTIONf_angle_d1.1793650
X-RAY DIFFRACTIONf_dihedral_angle_d8.0152034
X-RAY DIFFRACTIONf_chiral_restr0.06418
X-RAY DIFFRACTIONf_plane_restr0.008473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4901-2.74070.44471640.35063255X-RAY DIFFRACTION99
2.7407-3.13720.37041390.32663287X-RAY DIFFRACTION99
3.1372-3.95250.31941710.2723293X-RAY DIFFRACTION100
3.9525-58.97580.21791430.21363356X-RAY DIFFRACTION100

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