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- PDB-3tg1: Crystal structure of p38alpha in complex with a MAPK docking partner -

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Basic information

Entry
Database: PDB / ID: 3tg1
TitleCrystal structure of p38alpha in complex with a MAPK docking partner
Components
  • Dual specificity protein phosphatase 10
  • Mitogen-activated protein kinase 14
KeywordsTRANSFERASE/HYDROLASE / Kinase/Rhodanese-like domain / docking interaction / TRANSFERASE-HYDROLASE complex
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / p38MAPK events ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of adaptive immune response / regulation of brown fat cell differentiation / negative regulation of epithelial cell migration / negative regulation of p38MAPK cascade / 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 / negative regulation of oligodendrocyte differentiation / Regulation of TP53 Activity through Phosphorylation / Signaling by MAPK mutants / Myogenesis / RAF-independent MAPK1/3 activation / JUN kinase binding / VEGFA-VEGFR2 Pathway / negative regulation of JNK cascade / negative regulation of stress-activated MAPK cascade / regulation of synaptic membrane adhesion / positive regulation of regulatory T cell differentiation / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / dephosphorylation / cartilage condensation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / oligodendrocyte differentiation / phosphatase activity / fatty acid oxidation / cellular response to lipoteichoic acid / response to muramyl dipeptide / response to dietary excess / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / negative regulation of respiratory burst involved in inflammatory response / JUN kinase activity / mitogen-activated protein kinase / negative regulation of hippo signaling / chondrocyte differentiation / 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 / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / Neutrophil degranulation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / negative regulation of cell migration / DNA damage checkpoint signaling / cellular response to ionizing radiation / positive regulation of D-glucose import / stem cell differentiation / response to insulin / placenta development / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / cell morphogenesis / bone development / cellular response to virus / positive regulation of protein import into nucleus / glucose metabolic process / spindle pole / negative regulation of epithelial cell proliferation
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain ...Mitogen-activated protein (MAP) kinase phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase 14 / Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsZhang, Y.Y. / Wu, J.W. / Wang, Z.X.
CitationJournal: Sci.Signal. / Year: 2011
Title: A Distinct Interaction Mode Revealed by the Crystal Structure of the Kinase p38alpha with the MAPK Binding Domain of the Phosphatase MKP5.
Authors: Zhang, Y.Y. / Wu, J.W. / Wang, Z.X.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)61,5842
Polymers61,5842
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-3 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.428, 72.428, 226.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 43509.508 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 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P47811, mitogen-activated protein kinase
#2: Protein Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 18074.928 Da / Num. of mol.: 1 / Fragment: KBD (UNP RESIDUES 139-288)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Tris pH7.5, 9% [w/v] polyethylene glycol 3350, 8% [w/v] sucrose, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.7→36.214 Å / Num. obs: 17026 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.58 / Num. unique all: 1565 / % possible all: 93.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P38, 2OUC

1p38
PDB Unreleased entry

2ouc


Resolution: 2.71→36.214 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 854 5.04 %Random
Rwork0.2162 ---
all0.311 17026 --
obs0.2183 16942 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.609 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 88.8 Å2
Baniso -1Baniso -2Baniso -3
1-11.7137 Å20 Å2-0 Å2
2--11.7137 Å20 Å2
3----19.7893 Å2
Refinement stepCycle: LAST / Resolution: 2.71→36.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 0 15 3758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083820
X-RAY DIFFRACTIONf_angle_d1.2545171
X-RAY DIFFRACTIONf_dihedral_angle_d20.1581430
X-RAY DIFFRACTIONf_chiral_restr0.074578
X-RAY DIFFRACTIONf_plane_restr0.006666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7102-2.87990.31991330.2896252495
2.8799-3.10220.35071450.25532646100
3.1022-3.41420.30331350.24632683100
3.4142-3.90770.26591570.20542665100
3.9077-4.92130.21241500.17342735100
4.9213-36.21720.23971340.2139283597

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