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- PDB-9cj2: Dual phosphorylated human p38 alpha -

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Basic information

Entry
Database: PDB / ID: 9cj2
TitleDual phosphorylated human p38 alpha
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / MAPK14 / kinase / phosphorylated
Function / homology
Function and homology information


stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / CD163 mediating an anti-inflammatory response / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA ...stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / CD163 mediating an anti-inflammatory response / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / cellular response to UV-B / positive regulation of muscle cell differentiation / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / Myogenesis / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / Activation of the AP-1 family of transcription factors / p38MAPK cascade / ERK/MAPK targets / Regulation of MITF-M-dependent genes involved in pigmentation / fatty acid oxidation / MAP kinase kinase activity / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / signal transduction in response to DNA damage / 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 / skeletal muscle tissue development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / 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 / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / cell morphogenesis / bone development / cellular response to virus / platelet activation / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / glucose metabolic process / spindle pole / chemotaxis / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / cellular senescence / ADP signalling through P2Y purinoceptor 1 / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / secretory granule lumen / Oxidative Stress Induced Senescence / angiogenesis / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm
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
DI(HYDROXYETHYL)ETHER / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsStadnicki, E.J. / Ludewig, H. / Prem Kumar, R. / Kern, D. / Bradshaw, N.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Biorxiv / Year: 2024
Title: Dual-Action Kinase Inhibitors Influence p38 alpha MAP Kinase Dephosphorylation.
Authors: Stadnicki, E.J. / Ludewig, H. / Kumar, R.P. / Wang, X. / Qiao, Y. / Kern, D. / Bradshaw, N.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1754
Polymers83,0062
Non-polymers1682
Water905
1
A: Mitogen-activated protein kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6713
Polymers41,5031
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 14


Theoretical massNumber of molelcules
Total (without water)41,5031
Polymers41,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.595, 96.296, 220.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAP kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSAID- ...MAP kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSAID-binding protein / CSBP / MAP kinase MXI2 / MAX-interacting protein 2 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Stress-activated protein kinase 2a / SAPK2a


Mass: 41503.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8mg/mL phosphorylated p38 alpha set at a 1:1 ratio with 100 mM MES pH 6.5, 200 mM ammonium sulfate, 4% 1,3-Propanediol, and 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.03096 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 3, 2023
RadiationMonochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03096 Å / Relative weight: 1
ReflectionResolution: 2.82→48.15 Å / Num. obs: 26902 / % possible obs: 99.59 % / Redundancy: 6.2 % / Biso Wilson estimate: 94.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.061 / Rrim(I) all: 0.151 / Net I/σ(I): 7.8
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2606 / CC1/2: 0.29 / % possible all: 98.04

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→47.04 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3083 1201 5.01 %
Rwork0.2801 --
obs0.2815 23957 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.83→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 11 5 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035706
X-RAY DIFFRACTIONf_angle_d0.6127742
X-RAY DIFFRACTIONf_dihedral_angle_d11.9012117
X-RAY DIFFRACTIONf_chiral_restr0.041871
X-RAY DIFFRACTIONf_plane_restr0.005982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.940.4421340.4252438X-RAY DIFFRACTION99
2.94-3.080.44341230.43332492X-RAY DIFFRACTION100
3.08-3.240.39471150.4062512X-RAY DIFFRACTION100
3.24-3.440.3661380.34422494X-RAY DIFFRACTION100
3.44-3.710.361500.32192479X-RAY DIFFRACTION100
3.71-4.080.32011510.29382510X-RAY DIFFRACTION100
4.08-4.670.27581210.25512543X-RAY DIFFRACTION100
4.67-5.880.25761370.26022575X-RAY DIFFRACTION100
5.88-47.040.28951320.2352713X-RAY DIFFRACTION99
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)
15.064-2.2353-2.74535.92031.90014.80970.07580.68-0.6174-0.6171-0.65610.37980.2673-0.44790.57931.42940.18360.13680.72940.06510.6587-5.42437.90711.583
27.3105-0.4795.10963.0354-2.09710.62830.151-1.0654-0.729-0.2933-0.259-0.08660.4635-0.06040.12891.0240.11160.1840.91860.20470.65232.93432.86930.387
33.567-0.94342.21022.3683-1.38375.87580.0687-1.029-0.24060.0539-0.1205-0.4096-0.41080.84750.07210.8382-0.04110.14911.24110.24080.95266.61937.89737.604
47.8725-1.71790.39456.8067-0.98410.0681-0.3865-1.9562-0.88460.73770.32120.40621.2767-0.8110.12191.0991-0.00730.10291.7008-0.01090.623416.37468.74244.815
58.1221-1.8450.40648.20930.83737.2597-0.1391-1.90930.5962-0.06930.01550.19930.3493-0.88680.12580.6182-0.08150.05121.1112-0.31940.618323.44974.09235.393
63.6913-1.18462.75857.0233-3.90583.2006-1.2437-1.13340.09810.34561.53012.1446-0.6014-2.0520.03760.910.15760.08882.4429-0.28931.42334.73583.38834.757
77.8519-1.71212.16286.0542-1.67574.7288-0.1507-0.37770.3295-1.11790.07390.34490.2376-0.90340.17411.027-0.2583-0.05080.6409-0.15980.76559.98682.73618.988
81.7792-1.30070.11022.79522.15196.24430.05440.44190.7526-0.85390.13820.08910.0483-0.1233-0.17771.6484-0.2112-0.15060.91450.18961.28113.23985.4713.577
93.002-2.37141.17593.3091-1.81063.0829-0.6598-0.06091.6786-0.54960.2995-0.9288-0.52690.1450.39381.0152-0.1745-0.17550.7294-0.16161.436423.4985.43923.738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 5:77 )B5 - 77
2X-RAY DIFFRACTION2( CHAIN B AND RESID 78:239 )B78 - 239
3X-RAY DIFFRACTION3( CHAIN B AND RESID 240:352 )B240 - 352
4X-RAY DIFFRACTION4( CHAIN A AND RESID 4:42 )A4 - 42
5X-RAY DIFFRACTION5( CHAIN A AND RESID 43:102 )A43 - 102
6X-RAY DIFFRACTION6( CHAIN A AND RESID 103:123 )A103 - 123
7X-RAY DIFFRACTION7( CHAIN A AND RESID 124:239 )A124 - 239
8X-RAY DIFFRACTION8( CHAIN A AND RESID 240:288 )A240 - 288
9X-RAY DIFFRACTION9( CHAIN A AND RESID 289:352 )A289 - 352

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