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

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Basic information

Entry
Database: PDB / ID: 8acm
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 / response to dietary excess / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / 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 / 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 / osteoclast differentiation / positive regulation of erythrocyte differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / 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 / 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: 2.14 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 1.1Nov 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,7015
Polymers41,2511
Non-polymers4504
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-23 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.320, 75.160, 78.670
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 0.1,M HEPES pH 7.5, 25,%w/v PEG 3350 / Temp details: 4 deg C

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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: Eliptically 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: 2.14→78.67 Å / Num. obs: 20793 / % possible obs: 94.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.6
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2973 / % possible all: 93.9

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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: 2.14→54.345 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.481 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.271 / ESU R Free: 0.209
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1053 5.119 %0
Rwork0.2011 19518 --
all0.203 ---
obs-20571 93.556 %-
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: 45.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.586 Å2-0 Å2-0 Å2
2---1.654 Å20 Å2
3---2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.14→54.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 30 142 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132819
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152680
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.6373828
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5786164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89622.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26115487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0561518
X-RAY DIFFRACTIONr_chiral_restr0.0570.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
X-RAY DIFFRACTIONr_nbd_refined0.1930.2554
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.22545
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21364
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.214
X-RAY DIFFRACTIONr_nbd_other0.1750.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.25
X-RAY DIFFRACTIONr_mcbond_it2.9314.6581346
X-RAY DIFFRACTIONr_mcbond_other2.9324.6551345
X-RAY DIFFRACTIONr_mcangle_it4.5546.9761679
X-RAY DIFFRACTIONr_mcangle_other4.5536.981680
X-RAY DIFFRACTIONr_scbond_it3.125.0331473
X-RAY DIFFRACTIONr_scbond_other3.1195.0321474
X-RAY DIFFRACTIONr_scangle_it5.0717.4112149
X-RAY DIFFRACTIONr_scangle_other5.077.4112150
X-RAY DIFFRACTIONr_lrange_it7.82154.2273144
X-RAY DIFFRACTIONr_lrange_other7.78454.1283126
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
2.14-2.1960.261650.24515180.24515840.8670.89199.93690.232
2.196-2.2560.311410.26912250.27115750.8920.88780.3810.259
2.256-2.3210.282590.23710290.23915140.8860.91371.86260.227
2.321-2.3920.328540.22714300.23114850.8680.999.93270.214
2.392-2.470.228730.20613320.20714060.9140.92499.92890.196
2.47-2.5570.246720.20613060.20813780.9220.9271000.196
2.557-2.6530.221760.19812630.19913400.9280.93699.92540.192
2.653-2.7610.281640.2179450.22112980.9010.91977.7350.213
2.761-2.8840.252600.19611880.19912480.8970.9341000.196
2.884-3.0240.256600.20411360.20711980.9170.93499.83310.206
3.024-3.1870.27520.19910600.20211120.9050.9361000.203
3.187-3.380.266590.20610050.20910640.9190.9371000.216
3.38-3.6120.231540.28390.20210300.9310.94686.6990.212
3.612-3.90.211410.1927500.1939440.9380.94583.79240.216
3.9-4.270.239460.1827430.1868830.9260.94189.35450.207
4.27-4.770.209430.1627540.1647980.9570.96699.87470.185
4.77-5.5010.206390.1846850.1857240.9660.9651000.216
5.501-6.7210.265420.2255680.2286100.9390.9451000.255
6.721-9.4320.222320.1964610.1984950.9370.95299.5960.235
9.432-54.3450.312210.2172810.2213020.9110.9611000.336

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