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- PDB-5eta: Structure of MAPK14 with bound the KIM domain of the Toxoplasma p... -

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Basic information

Entry
Database: PDB / ID: 5eta
TitleStructure of MAPK14 with bound the KIM domain of the Toxoplasma protein GRA24
Components
  • Mitogen-activated protein kinase 14
  • Putative transmembrane protein
KeywordsTRANSFERASE / MAPK14 / Gra24 / KIM domain / peptide-protein complex
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 / stress-induced premature senescence / CD163 mediating an anti-inflammatory response / 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 / stress-induced premature senescence / CD163 mediating an anti-inflammatory response / 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 / mitogen-activated protein kinase p38 binding / Platelet sensitization by LDL / Myogenesis / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / D-glucose import / 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 / positive regulation of D-glucose import / cellular response to ionizing radiation / 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. / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative transmembrane protein / Putative transmembrane protein / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPellegrini, E. / Palencia, A. / Braun, L. / Kapp, U. / Bougdour, A. / Belrhali, H. / Bowler, M.W. / Hakimi, M.
CitationJournal: Structure / Year: 2017
Title: Structural Basis for the Subversion of MAP Kinase Signaling by an Intrinsically Disordered Parasite Secreted Agonist.
Authors: Pellegrini, E. / Palencia, A. / Braun, L. / Kapp, U. / Bougdour, A. / Belrhali, H. / Bowler, M.W. / Hakimi, M.A.
History
DepositionNov 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mitogen-activated protein kinase 14
D: Putative transmembrane protein
A: Mitogen-activated protein kinase 14
C: Putative transmembrane protein


Theoretical massNumber of molelcules
Total (without water)86,3154
Polymers86,3154
Non-polymers00
Water23413
1
B: Mitogen-activated protein kinase 14
D: Putative transmembrane protein


Theoretical massNumber of molelcules
Total (without water)43,1572
Polymers43,1572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-7 kcal/mol
Surface area17380 Å2
MethodPISA
2
A: Mitogen-activated protein kinase 14
C: Putative transmembrane protein


Theoretical massNumber of molelcules
Total (without water)43,1572
Polymers43,1572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.091, 61.900, 75.671
Angle α, β, γ (deg.)105.62, 96.31, 114.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / ...MAPK 14 / Cytokine suppressive anti-inflammatory drug-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: 41343.195 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 (E. coli)
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Protein/peptide Putative transmembrane protein


Mass: 1814.135 Da / Num. of mol.: 2 / Fragment: UNP residues 440-455 / Source method: obtained synthetically / Details: peptide / Source: (synth.) Toxoplasma gondii (eukaryote) / References: UniProt: A0A086L2F3, UniProt: B6KJB6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1M Tris/HCl pH 8.5, 25-28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→45.79 Å / Num. obs: 43826 / % possible obs: 96.6 % / Redundancy: 1.9 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→40.132 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2903 983 5.17 %
Rwork0.2188 --
obs0.2226 18997 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→40.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5672 0 0 13 5685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045805
X-RAY DIFFRACTIONf_angle_d0.9627877
X-RAY DIFFRACTIONf_dihedral_angle_d8.7665470
X-RAY DIFFRACTIONf_chiral_restr0.057885
X-RAY DIFFRACTIONf_plane_restr0.0071007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.41351550.33552573X-RAY DIFFRACTION97
2.9476-3.13220.36461350.30592603X-RAY DIFFRACTION97
3.1322-3.37390.33641460.27692566X-RAY DIFFRACTION97
3.3739-3.71320.34011220.22852624X-RAY DIFFRACTION96
3.7132-4.250.2521440.18792528X-RAY DIFFRACTION96
4.25-5.35260.23361290.17192580X-RAY DIFFRACTION96
5.3526-40.13640.25911520.18592540X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -0.6212 Å / Origin y: 9.6315 Å / Origin z: -17.2115 Å
111213212223313233
T0.2654 Å20.0067 Å20.0081 Å2-0.372 Å2-0.0388 Å2--0.3163 Å2
L0.1886 °20.0629 °20.0394 °2-1.2219 °2-0.6299 °2--0.1021 °2
S-0.0383 Å °-0.0266 Å °0.0175 Å °-0.0371 Å °0.0401 Å °-0.1045 Å °0.0268 Å °0.01 Å °-0.0131 Å °
Refinement TLS groupSelection details: all

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