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- PDB-5etf: Structure of dead kinase MAPK14 with bound the KIM domain of MKK6 -

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Basic information

Entry
Database: PDB / ID: 5etf
TitleStructure of dead kinase MAPK14 with bound the KIM domain of MKK6
Components
  • Dual specificity mitogen-activated protein kinase kinase 6
  • Mitogen-activated protein kinase 14
KeywordsTRANSFERASE / MAPK14 / MKk6 / KIM domain / peptide-protein complex
Function / homology
Function and homology information


nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / positive regulation of cyclase activity / : / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / stress-induced premature senescence / negative regulation of cold-induced thermogenesis / positive regulation of myoblast fusion / cartilage condensation ...nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / mitogen-activated protein kinase kinase / positive regulation of cyclase activity / : / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of synaptic membrane adhesion / stress-induced premature senescence / negative regulation of cold-induced thermogenesis / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / CD163 mediating an anti-inflammatory response / cell surface receptor protein serine/threonine kinase signaling pathway / response to dietary excess / positive regulation of myotube differentiation / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of muscle cell differentiation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / Myogenesis / response to muramyl dipeptide / Platelet sensitization by LDL / NFAT protein binding / cellular response to lipoteichoic acid / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / p38MAPK cascade / fatty acid oxidation / ERK/MAPK targets / PI5P Regulates TP53 Acetylation / MAP kinase kinase activity / chondrocyte differentiation / Regulation of MITF-M-dependent genes involved in pigmentation / cellular response to vascular endothelial growth factor stimulus / skeletal muscle tissue development / regulation of ossification / MAP kinase activity / Uptake and function of anthrax toxins / mitogen-activated protein kinase / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / RHO GTPases Activate NADPH Oxidases / positive regulation of myoblast differentiation / negative regulation of hippo signaling / positive regulation of cardiac muscle cell proliferation / response to muscle stretch / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of brown fat cell differentiation / striated muscle cell differentiation / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / p38MAPK events / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / stem cell differentiation / regulation of signal transduction by p53 class mediator / positive regulation of D-glucose import across plasma membrane / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / activated TAK1 mediates p38 MAPK activation / negative regulation of inflammatory response to antigenic stimulus / negative regulation of canonical Wnt signaling pathway / cellular response to virus / cell morphogenesis / platelet activation / bone development / response to insulin / glucose metabolic process / NOD1/2 Signaling Pathway / positive regulation of protein import into nucleus / PKR-mediated signaling / VEGFA-VEGFR2 Pathway / cellular senescence / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / chemotaxis / spindle pole / Interleukin-1 signaling / MAPK cascade / transcription by RNA polymerase II / ADP signalling through P2Y purinoceptor 1 / cellular response to lipopolysaccharide / angiogenesis / protein tyrosine kinase activity / secretory granule lumen / protein phosphatase binding / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / ficolin-1-rich granule lumen / cytoskeleton / regulation of cell cycle / cell surface receptor signaling pathway / nuclear speck / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression
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 / Serine/threonine-protein kinase, active site ...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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Dual specificity mitogen-activated protein kinase kinase 6 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Mitogen-activated protein kinase 14
B: Dual specificity mitogen-activated protein kinase kinase 6


Theoretical massNumber of molelcules
Total (without water)42,9992
Polymers42,9992
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.383, 82.383, 123.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-586-

HOH

31A-615-

HOH

41A-616-

HOH

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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: 41371.211 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
#2: Protein/peptide Dual specificity mitogen-activated protein kinase kinase 6 / MAPKK 6 / MAPK/ERK kinase 6 / MEK 6 / Stress-activated protein kinase kinase 3 / SAPKK3


Mass: 1628.015 Da / Num. of mol.: 1 / Fragment: UNP residues 4-18 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P52564, mitogen-activated protein kinase kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% (w/v) PEG 3350 and 0.1 mM Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 32069 / % possible obs: 90.3 % / Redundancy: 3.9 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 59

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.655 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.78 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1634 5.1 %
Rwork0.1629 --
obs0.1662 32069 87.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 0 223 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082918
X-RAY DIFFRACTIONf_angle_d0.9293962
X-RAY DIFFRACTIONf_dihedral_angle_d12.6291769
X-RAY DIFFRACTIONf_chiral_restr0.055443
X-RAY DIFFRACTIONf_plane_restr0.006509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.47070.2991840.26111403X-RAY DIFFRACTION49
2.4707-2.55040.33291010.24571664X-RAY DIFFRACTION58
2.5504-2.64160.2887820.24022006X-RAY DIFFRACTION68
2.6416-2.74730.26881570.22432436X-RAY DIFFRACTION85
2.7473-2.87240.27641290.20522824X-RAY DIFFRACTION98
2.8724-3.02380.29811880.19952859X-RAY DIFFRACTION99
3.0238-3.21320.22751540.1912852X-RAY DIFFRACTION99
3.2132-3.46120.24631520.16772873X-RAY DIFFRACTION99
3.4612-3.80940.22321540.13832861X-RAY DIFFRACTION99
3.8094-4.36020.17351430.12232908X-RAY DIFFRACTION99
4.3602-5.49210.18561520.12142878X-RAY DIFFRACTION100
5.4921-46.66380.20181380.14392871X-RAY DIFFRACTION99

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