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- PDB-2onl: Crystal Structure of the p38a-MAPKAP kinase 2 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 2onl
TitleCrystal Structure of the p38a-MAPKAP kinase 2 Heterodimer
Components
  • MAP kinase-activated protein kinase 2
  • Mitogen-activated protein kinase 14
KeywordsTRANSFERASE / heterodimer / kinase / NLS / NES / docking groove
Function / homology
Function and homology information


macropinocytosis / calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / stress-activated protein kinase signaling cascade ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / positive regulation of macrophage cytokine production / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / positive regulation of myoblast fusion / toll-like receptor signaling pathway / cellular response to UV-B / Platelet sensitization by LDL / positive regulation of muscle cell differentiation / mitogen-activated protein kinase p38 binding / Myogenesis / NFAT protein binding / positive regulation of myotube differentiation / D-glucose import / regulation of cytokine production involved in inflammatory response / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / p38MAPK cascade / Regulation of MITF-M-dependent genes involved in pigmentation / MAP kinase kinase activity / fatty acid oxidation / cellular response to lipoteichoic acid / inner ear development / 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 / Regulation of HSF1-mediated heat shock response / mitogen-activated protein kinase / JUN kinase activity / negative regulation of hippo signaling / chondrocyte differentiation / positive regulation of myoblast differentiation / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / 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 / regulation of mRNA stability / positive regulation of interleukin-12 production / response to cytokine / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / cellular response to ionizing radiation / positive regulation of D-glucose import / activated TAK1 mediates p38 MAPK activation / stem cell differentiation / response to insulin / placenta development / negative regulation of inflammatory response to antigenic stimulus / Regulation of TNFR1 signaling / negative regulation of canonical Wnt signaling pathway / NOD1/2 Signaling Pathway / cell morphogenesis / bone development / platelet activation / cellular response to virus / spindle pole / VEGFA-VEGFR2 Pathway / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / osteoblast differentiation / positive regulation of tumor necrosis factor production / cellular senescence / MAPK cascade / ADP signalling through P2Y purinoceptor 1 / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / peptidyl-serine phosphorylation / protein phosphatase binding
Similarity search - Function
Protein kinase-like (PK-like) / MAP kinase activated protein kinase 2 / 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. / : / Few Secondary Structures / Irregular ...Protein kinase-like (PK-like) / MAP kinase activated protein kinase 2 / 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. / : / Few Secondary Structures / Irregular / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
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: 4 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 24, 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 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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 / 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
C: MAP kinase-activated protein kinase 2
B: Mitogen-activated protein kinase 14
D: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)176,5694
Polymers176,5694
Non-polymers00
Water00
1
A: Mitogen-activated protein kinase 14
C: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)88,2842
Polymers88,2842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-18 kcal/mol
Surface area31960 Å2
MethodPISA
2
B: Mitogen-activated protein kinase 14
D: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)88,2842
Polymers88,2842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-9 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.150, 103.150, 231.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Mitogen-activated protein kinase 14 / 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 MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 46285.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pBEV / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49137, non-specific serine/threonine protein kinase

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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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 3.75% Peg 2000, 100mM Hepes, Prior to crystallization, 1-s-nonyl-1-b-D-thioglucoside (1xcmc) and heptanetriol (1.5%) was added to the protein sample, pH 7.5, VAPOR DIFFUSION, HANGING DROP, ...Details: 3.75% Peg 2000, 100mM Hepes, Prior to crystallization, 1-s-nonyl-1-b-D-thioglucoside (1xcmc) and heptanetriol (1.5%) was added to the protein sample, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→45.32 Å / Num. obs: 19566 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 2.79 % / Biso Wilson estimate: 72.78 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 5.1
Reflection shellResolution: 4→4.14 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.368 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
d*TREKdata reduction
CNXphasing
BUSTER-TNTV. 1.1.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OKR, 1KWP

2okr

1kwp


Resolution: 4→45.34 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: REFINEMENT WAS LIMITED TO RIGID BODY DUE TO THE LOW RESOLUTION OF THE DATA
RfactorNum. reflection% reflectionSelection details
Rfree0.331 984 5.03 %RANDOM
Rwork0.314 ---
obs0.315 19566 95.6 %-
all-20550 --
Displacement parametersBiso mean: 99.77 Å2
Baniso -1Baniso -2Baniso -3
1--22.06 Å20 Å20 Å2
2---22.06 Å20 Å2
3---44.12 Å2
Refine analyzeLuzzati coordinate error obs: 1.17 Å
Refinement stepCycle: LAST / Resolution: 4→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10466 0 0 0 10466
LS refinement shellResolution: 4→4.24 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3098 172 5.49 %
Rwork0.2996 2959 -
all30.01 3131 -
obs--95.62 %

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