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- PDB-8aco: Crystal structure of WT p38alpha -

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Basic information

Entry
Database: PDB / ID: 8aco
TitleCrystal structure of WT p38alpha
ComponentsMitogen-activated protein kinase 14
KeywordsONCOPROTEIN / kinase / enzyme / inhibitor
Function / homology
Function and homology information


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 ...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 / VEGFA-VEGFR2 Pathway / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 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 / fatty acid oxidation / response to dietary excess / cellular response to lipoteichoic acid / response to muramyl dipeptide / MAP kinase activity / regulation of ossification / 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 / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / response to muscle stretch / striated muscle cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import / cellular response to ionizing radiation / 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 / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / 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 / transcription by RNA polymerase II / protein kinase activity / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase 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. ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase 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
Similarity search - Domain/homology
Chem-SB2 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPous, J. / Baginski, B. / Gonzalez, L. / Macias, M.J. / Nebreda, A.R.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109521RB-100 Spain
La Caixa FoundationBioMedTec VIII - Nebre Spain
CitationJournal: Res Sq
Title: Crystal structure of WT p38alpha
Authors: Pous, J. / Baginski, B. / Gonzalez, L. / Macias, M.J. / Nebreda, A.R.
History
DepositionJul 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6774
Polymers41,2511
Non-polymers4263
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-23 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 74.612, 78.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 41251.082 Da / Num. of mol.: 1
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: Chemical ChemComp-SB2 / 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE


Mass: 377.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16FN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1,M HEPES pH 7, 15 %w/v PEG 4000
Temp details: moved to 293K after 2 weeks

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryosystems 700 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020 / Details: Elliptically bent mirror
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.65→78.1 Å / Num. obs: 10940 / % possible obs: 94.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1395 / % possible all: 84.1

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Processing

Software
NameVersionClassification
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOO

4loo


Resolution: 2.65→53.95 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 17.107 / SU ML: 0.336 / Cross valid method: FREE R-VALUE / ESU R Free: 0.402
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 532 4.9 %0
Rwork0.2087 10326 --
all0.212 ---
obs-10858 93.773 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 57.757 Å2
Baniso -1Baniso -2Baniso -3
1--1.646 Å2-0 Å2-0 Å2
2---4.077 Å20 Å2
3---5.723 Å2
Refinement stepCycle: LAST / Resolution: 2.65→53.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 29 112 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132814
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152665
X-RAY DIFFRACTIONr_angle_refined_deg1.211.6383825
X-RAY DIFFRACTIONr_angle_other_deg1.0271.5786132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9495336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72122.303152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72915485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5911518
X-RAY DIFFRACTIONr_chiral_restr0.0430.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_nbd_refined0.1780.2625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.22611
X-RAY DIFFRACTIONr_nbtor_refined0.1560.21323
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.212
X-RAY DIFFRACTIONr_nbd_other0.1590.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.23
X-RAY DIFFRACTIONr_mcbond_it2.2696.1021338
X-RAY DIFFRACTIONr_mcbond_other2.276.0991337
X-RAY DIFFRACTIONr_mcangle_it3.979.1461670
X-RAY DIFFRACTIONr_mcangle_other3.9699.1491671
X-RAY DIFFRACTIONr_scbond_it1.8366.3051476
X-RAY DIFFRACTIONr_scbond_other1.8366.3041477
X-RAY DIFFRACTIONr_scangle_it3.2949.3782153
X-RAY DIFFRACTIONr_scangle_other3.2939.3782154
X-RAY DIFFRACTIONr_lrange_it7.80570.443163
X-RAY DIFFRACTIONr_lrange_other7.79170.4223151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.65-2.7190.55310.3835390.3938380.6150.64968.01910.356
2.719-2.7930.327490.3017660.3028150.7360.751000.278
2.793-2.8740.329470.2597530.2638010.7460.83499.87520.234
2.874-2.9620.321270.2537390.2557660.7970.8511000.233
2.962-3.0590.337360.2297030.2347400.8390.87999.86490.21
3.059-3.1660.331370.226940.2267310.8780.8941000.2
3.166-3.2850.319330.2176800.227130.7870.9051000.202
3.285-3.4180.304330.2436400.2466800.8720.88398.97060.229
3.418-3.570.387160.2464700.2516400.8030.88375.93750.232
3.57-3.7430.328200.2274610.2316330.8590.89775.98740.214
3.743-3.9450.365150.2214480.2255990.8410.90977.29550.209
3.945-4.1830.205240.1735310.1745560.9380.94899.82010.169
4.183-4.4690.163330.1535060.1545390.9590.961000.151
4.469-4.8250.226320.1574610.1614930.9490.961000.154
4.825-5.2810.268250.1574490.1634740.9310.9621000.161
5.281-5.8970.221200.1913960.1924160.9350.9511000.189
5.897-6.7960.561150.1933720.2013870.7640.9461000.19
6.796-8.2910.151120.1743140.1733270.9580.95699.69420.179
8.291-11.5890.248250.1632360.1712610.9430.9691000.172
11.589-53.950.28720.2781680.27817010.9371000.292

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