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- PDB-8yp8: Structure of the p38alpha-pepHePTPm(16-31)(V31C ) complex -

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Basic information

Entry
Database: PDB / ID: 8yp8
TitleStructure of the p38alpha-pepHePTPm(16-31)(V31C ) complex
Components
  • Mitogen-activated protein kinase 14
  • Tyrosine-protein phosphatase non-receptor type 7
KeywordsTRANSFERASE / MAP KINASE P38 ALPHA / docking interactions
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 / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 ...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 / NLRP1 inflammasome complex assembly / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / Myogenesis / Regulation of TP53 Activity through Phosphorylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / response to muramyl dipeptide / VEGFA-VEGFR2 Pathway / regulation of ossification / Interleukin-37 signaling / chondrocyte differentiation / fatty acid oxidation / striated muscle cell differentiation / regulation of synaptic membrane adhesion / stress-induced premature senescence / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / skeletal muscle tissue development / positive regulation of cyclase activity / response to dietary excess / positive regulation of myotube differentiation / protein dephosphorylation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / NFAT protein binding / cellular response to lipoteichoic acid / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / positive regulation of cardiac muscle cell proliferation / non-membrane spanning protein tyrosine phosphatase activity / response to muscle stretch / lipopolysaccharide-mediated signaling pathway / cellular response to vascular endothelial growth factor stimulus / MAP kinase activity / mitogen-activated protein kinase / vascular endothelial growth factor receptor signaling pathway / positive regulation of brown fat cell differentiation / pyroptotic inflammatory response / stress-activated MAPK cascade / negative regulation of hippo signaling / positive regulation of myoblast differentiation / placenta development / osteoclast differentiation / positive regulation of interleukin-12 production / cell morphogenesis / DNA damage checkpoint signaling / signal transduction in response to DNA damage / protein-tyrosine-phosphatase / positive regulation of D-glucose import across plasma membrane / Neutrophil degranulation / positive regulation of erythrocyte differentiation / protein tyrosine phosphatase activity / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to tumor necrosis factor / glucose metabolic process / cellular response to virus / protein maturation / positive regulation of protein import into nucleus / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / peptidyl-serine phosphorylation / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / cytoplasmic side of plasma membrane / spindle pole / kinase activity / MAPK cascade / Negative regulation of MAPK pathway / protein autophosphorylation / cellular response to lipopolysaccharide / angiogenesis / response to lipopolysaccharide / protein phosphatase binding / cytoskeleton / protein kinase activity / protein phosphorylation / nuclear speck / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / regulation of transcription by RNA polymerase II / DNA damage response / regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding
Similarity search - Function
Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain ...Protein-tyrosine phosphatase, KIM-containing / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / 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
Tyrosine-protein phosphatase non-receptor type 7 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsZhang, Y.Y. / Pei, C.J. / He, Q.Q. / Luo, Z.P. / Wu, J.W. / Wang, Z.X.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0802500 China
Ministry of Science and Technology (MoST, China)2022YFA0806504 China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into the allosteric activation of p38alpha MAP kinase via specific docking interactions
Authors: Zhang, Y.Y. / Pei, C.J. / He, Q.Q. / Luo, Z.P. / Wu, J.W. / Wang, Z.X.
History
DepositionMar 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: 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: Tyrosine-protein phosphatase non-receptor type 7


Theoretical massNumber of molelcules
Total (without water)45,2422
Polymers45,2422
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-7 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.960, 81.960, 122.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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: 43378.312 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: Protein/peptide Tyrosine-protein phosphatase non-receptor type 7 / KIM peptide derived from HePTP / Hematopoietic protein-tyrosine phosphatase / HEPTP / Protein- ...KIM peptide derived from HePTP / Hematopoietic protein-tyrosine phosphatase / HEPTP / Protein-tyrosine phosphatase LC-PTP


Mass: 1864.180 Da / Num. of mol.: 1 / Mutation: V31C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35236, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M HEPES pH 7.8 0.6-0.8 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.14→46.35 Å / Num. obs: 26386 / % possible obs: 98 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.047 / Net I/σ(I): 18.9
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1741 / CC1/2: 0.482 / Rpim(I) all: 0.552 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p38

1p38
PDB Unreleased entry


Resolution: 2.14→46.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.654 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1290 4.9 %RANDOM
Rwork0.1862 ---
obs0.1876 25056 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.46 Å2 / Biso mean: 37.56 Å2 / Biso min: 18.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å2-0 Å2
2---0.34 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 2.14→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 0 221 3122
Biso mean---38.29 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132966
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152841
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.644020
X-RAY DIFFRACTIONr_angle_other_deg1.3491.586532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7321.89164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44115524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg161522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_mcbond_it3.5823.7371433
X-RAY DIFFRACTIONr_mcbond_other3.5833.7371432
X-RAY DIFFRACTIONr_mcangle_it5.4525.5811786
LS refinement shellResolution: 2.14→2.194 Å
RfactorNum. reflection% reflection
Rfree0.357 80 -
Rwork0.326 1470 -
obs--78.92 %

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