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- PDB-9nyt: Crystal structure of Human p38 alpha MAPK in Complex with MW01-32... -

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Basic information

Entry
Database: PDB / ID: 9nyt
TitleCrystal structure of Human p38 alpha MAPK in Complex with MW01-32-154JS
ComponentsMitogen-activated protein kinase 14
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE DOMAIN / ATP BINDING / PHOSPHORYLATION / CYTOSOL
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
: / ETHANEPEROXOIC ACID / 4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBrunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)NIH AG031311 NIH AG043415 United States
CitationJournal: To Be Published
Title: Crystal structure of Human p38 alpha MAPK in Complex with MW01-32-154JS
Authors: Brunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
History
DepositionMar 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,0756
Polymers44,0871
Non-polymers9875
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.670, 74.256, 79.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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: 44087.098 Da / Num. of mol.: 1
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 (E. coli)
References: UniProt: Q16539, mitogen-activated protein kinase

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-GG5 / 4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE


Mass: 239.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10FN3
#3: Chemical ChemComp-A1B7S / (3P)-3-(naphthalen-2-yl)-6-(piperazin-1-yl)-4-(pyridin-4-yl)pyridazine


Mass: 367.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N5
#4: Chemical ChemComp-F50 / ETHANEPEROXOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 45.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 10000 0.1M Ammonium Acetate 0.1M Bis-Tris (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2023 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.16→54.31 Å / Num. obs: 21392 / % possible obs: 97.9 % / Redundancy: 12.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.04 / Rrim(I) all: 0.144 / Χ2: 0.82 / Net I/σ(I): 10.2 / Num. measured all: 276544
Reflection shellResolution: 2.16→2.28 Å / % possible obs: 99.1 % / Redundancy: 12 % / Rmerge(I) obs: 2.036 / Num. measured all: 37283 / Num. unique obs: 3110 / CC1/2: 0.618 / Rpim(I) all: 0.606 / Rrim(I) all: 2.13 / Χ2: 0.81 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
REFMAC5.8.0425phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→42.11 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1073 5.04 %Random
Rwork0.193 ---
obs0.195 21288 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 68 92 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022859
X-RAY DIFFRACTIONf_angle_d0.5443884
X-RAY DIFFRACTIONf_dihedral_angle_d6.84405
X-RAY DIFFRACTIONf_chiral_restr0.04427
X-RAY DIFFRACTIONf_plane_restr0.004502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.260.38111370.32612488X-RAY DIFFRACTION98
2.26-2.380.30811530.26112512X-RAY DIFFRACTION99
2.38-2.530.2911700.23632499X-RAY DIFFRACTION100
2.53-2.720.29021140.22792481X-RAY DIFFRACTION95
2.72-2.990.25111340.21332564X-RAY DIFFRACTION100
2.99-3.420.25551180.20732555X-RAY DIFFRACTION100
3.43-4.320.20961190.162362X-RAY DIFFRACTION91
4.32-42.110.19371280.16372754X-RAY DIFFRACTION100
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)
17.5040.5742-0.30397.3114-1.3536.69360.1579-0.55630.29880.46490.30070.9871-0.6922-0.2671-0.42980.4637-0.01160.13810.50340.08740.8622-16.26160.505421.611
23.7690.20460.19173.0344-0.12562.02620.4416-0.23650.63960.9012-0.10350.618-1.0629-0.3033-0.2260.42460.00430.08940.2403-0.03290.4446-7.486711.157513.4347
36.5767-2.442.41823.251-1.78772.46320.3154-0.0064-0.8298-0.0532-0.0609-0.0850.17840.1366-0.16550.31380.02060.00170.2411-0.03080.4617-1.149-1.71429.6895
44.18391.8784-0.3711.10750.86344.05180.1344-0.18120.1362-0.11050.50330.8359-0.3552-0.9188-0.61380.3135-0.0056-0.00740.44750.10890.6697-15.03814.619112.3225
55.8704-6.20990.51857.503-0.86663.8484-0.9223-2.1606-0.95711.63151.33710.3191-0.35220.1691-0.3540.89930.02720.08540.81420.08760.767811.2817-4.618931.1365
65.19750.0505-0.02612.7971-0.07425.50010.0224-0.0137-0.2196-0.0695-0.14450.14080.275-0.0240.09690.32450.0012-0.01690.25350.0540.45599.534-2.819517.0469
76.82972.0460.63821.22641.11635.3767-0.11720.22121.2118-0.21210.41860.7678-1.1409-0.91850.06170.55020.0438-0.02110.49650.11170.825815.786513.332715.7661
84.60581.932-0.21465.6886-0.31862.07280.0442-0.0790.55990.1254-0.1373-0.3204-0.19670.10230.05670.30330.015-0.01810.3520.0270.533725.613313.108520.1375
94.8182-0.91481.31243.8484-0.82654.45670.1336-0.1095-0.36580.0119-0.2106-0.4570.0750.30120.06250.33010.05090.04690.38050.04260.502522.1182-4.158115.3349
105.7456-0.3195-0.6724.1653-0.43844.78930.44720.51520.3494-0.4728-0.16520.53520.0686-0.1288-0.26470.25980.0934-0.10240.35940.08060.3794-7.73828.35292.4276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 5 THROUGH 48 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 49 THROUGH 70 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 71 THROUGH 88 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 89 THROUGH 109 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 110 THROUGH 126 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 127 THROUGH 167 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 168 THROUGH 201 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 202 THROUGH 268 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 269 THROUGH 324 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 325 THROUGH 353 )

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