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- PDB-2okr: Crystal Structure of the P38a-MAPKAP kinase 2 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 2okr
TitleCrystal Structure of the P38a-MAPKAP kinase 2 Heterodimer
Components
  • MAP kinase-activated protein kinase 2
  • Mitogen-activated protein kinase 14MAPK14
KeywordsTRANSFERASE / Kinase / NLS / NES / heterodimer / docking groove
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cyclase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cyclase activity / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of interleukin-6 production / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / toll-like receptor signaling pathway / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / stress-activated protein kinase signaling cascade / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / response to dietary excess / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / inner ear development / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / regulation of ossification / MAP kinase activity / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / regulation of cellular response to heat / skeletal muscle tissue development / signal transduction in response to DNA damage / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of cardiac muscle cell proliferation / p38MAPK events / regulation of mRNA stability / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / placenta development / DNA damage checkpoint signaling / response to cytokine / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / Regulation of TNFR1 signaling / positive regulation of glucose import / negative regulation of canonical Wnt signaling pathway / response to insulin / NOD1/2 Signaling Pathway / bone development / cell morphogenesis / platelet activation / osteoblast differentiation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / MAPK cascade / cellular senescence / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / protein phosphatase binding / peptidyl-serine phosphorylation / angiogenesis / Oxidative Stress Induced Senescence
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...MAP kinase activated protein kinase, C-terminal / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
MAP kinase-activated protein kinase 2 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTer Haar, E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the P38alpha-MAPKAP kinase 2 heterodimer.
Authors: ter Haar, E. / Prabakhar, P. / Liu, X. / Lepre, C.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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
C: MAP kinase-activated protein kinase 2
D: Mitogen-activated protein kinase 14
F: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)89,6234
Polymers89,6234
Non-polymers00
Water3,549197
1
A: Mitogen-activated protein kinase 14
C: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)44,8112
Polymers44,8112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area17190 Å2
MethodPISA
2
D: Mitogen-activated protein kinase 14
F: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)44,8112
Polymers44,8112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.550, 81.550, 121.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAPK14 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Cytokine suppressive anti- ...Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Cytokine suppressive anti-inflammatory drug-binding protein / CSAID-binding protein / CSBP / MAX-interacting protein 2 / MAP kinase MXI2 / SAPK2A


Mass: 41998.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, MXI2 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Protein/peptide MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 2812.511 Da / Num. of mol.: 2 / Fragment: residues 370-393 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (Humans)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25% Peg 3350, 250 mM Sodium Formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40.78 Å / Num. obs: 60104 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.06 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.97 / Net I/σ(I): 9 / Scaling rejects: 1391
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.2 / Num. measured all: 13657 / Num. unique all: 5517 / Χ2: 1.15 / % possible all: 90.7

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å30.21 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
MOLREPphasing
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
autoBUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LEZ

1lez


Resolution: 2→8.48 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 2981 -random
Rwork0.2392 ---
all0.2385 ---
obs0.2385 60104 98.6 %-
Displacement parametersBiso mean: 16.049 Å2
Baniso -1Baniso -2Baniso -3
1-4.8961785 Å20 Å20 Å2
2--4.8961785 Å20 Å2
3----9.79235699 Å2
Refine analyzeLuzzati coordinate error obs: 0.2895 Å
Refinement stepCycle: LAST / Resolution: 2→8.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 0 197 5989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.193
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_torsion22.36
LS refinement shellResolution: 2→2.12 Å
RfactorNum. reflection% reflection
Rfree0.2644 468 -
Rwork0.2371 --
obs-9208 98.38 %

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