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- PDB-2oza: Structure of p38alpha complex -

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Basic information

Entry
Database: PDB / ID: 2oza
TitleStructure of p38alpha complex
Components
  • MAP kinase-activated protein kinase 2
  • Mitogen-activated protein kinase 14
KeywordsSIGNALING PROTEIN/TRANSFERASE / SERINE/THREONINE KINASE / PROTEIN-PROTEIN COMPLEX / P38A / MK2 / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 ...calcium-dependent protein serine/threonine kinase activity / CREB phosphorylation / macropinocytosis / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Regulation of MITF-M-dependent genes involved in pigmentation / NLRP1 inflammasome complex assembly / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / cell surface receptor protein serine/threonine kinase signaling pathway / ADP signalling through P2Y purinoceptor 1 / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / Myogenesis / Regulation of TP53 Activity through Phosphorylation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / regulation of tumor necrosis factor production / response to muramyl dipeptide / VEGFA-VEGFR2 Pathway / regulation of ossification / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / chondrocyte differentiation / fatty acid oxidation / striated muscle cell differentiation / regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase binding / regulation of synaptic membrane adhesion / stress-induced premature senescence / positive regulation of myoblast fusion / cartilage condensation / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / skeletal muscle tissue development / positive regulation of cyclase activity / response to dietary excess / positive regulation of myotube differentiation / cellular response to UV-B / mitogen-activated protein kinase p38 binding / toll-like receptor signaling pathway / NFAT protein binding / cellular response to lipoteichoic acid / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / positive regulation of cardiac muscle cell proliferation / response to muscle stretch / lipopolysaccharide-mediated signaling pathway / cellular response to vascular endothelial growth factor stimulus / MAP kinase activity / mitogen-activated protein kinase / vascular endothelial growth factor receptor signaling pathway / positive regulation of brown fat cell differentiation / pyroptotic inflammatory response / stress-activated MAPK cascade / Regulation of HSF1-mediated heat shock response / negative regulation of hippo signaling / positive regulation of myoblast differentiation / placenta development / osteoclast differentiation / positive regulation of interleukin-12 production / cell morphogenesis / DNA damage checkpoint signaling / regulation of cellular response to heat / signal transduction in response to DNA damage / regulation of mRNA stability / p38MAPK events / response to cytokine / positive regulation of D-glucose import across plasma membrane / Neutrophil degranulation / positive regulation of erythrocyte differentiation / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to tumor necrosis factor / glucose metabolic process / cellular response to virus / protein maturation / activated TAK1 mediates p38 MAPK activation / positive regulation of protein import into nucleus / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / Regulation of TNFR1 signaling / peptidyl-serine phosphorylation / VEGFA-VEGFR2 Pathway / positive regulation of reactive oxygen species metabolic process / osteoblast differentiation / spindle pole / kinase activity / MAPK cascade / protein autophosphorylation / cellular response to lipopolysaccharide / angiogenesis / response to lipopolysaccharide
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 / 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
Mitogen-activated protein kinase 14 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWhite, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis of MAPK-activated protein kinase 2:p38 assembly
Authors: White, A. / Pargellis, C.A. / Studts, J.M. / Werneburg, B.G. / Farmer II, B.T.
History
DepositionFeb 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: MAP kinase-activated protein kinase 2
B: Mitogen-activated protein kinase 14


Theoretical massNumber of molelcules
Total (without water)83,0832
Polymers83,0832
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-21 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 83.310, 231.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a heterodimer containing one p38alpha and one MK2 molecules

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Components

#1: Protein MAP kinase-activated protein kinase 2 / E.C.2.7.11.1 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 40983.469 Da / Num. of mol.: 1 / Fragment: MK2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Protein Mitogen-activated protein kinase 14 / E.C.2.7.11.24 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / CRK1


Mass: 42099.969 Da / Num. of mol.: 1 / Fragment: P38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapk14, Crk1, Csbp1, Csbp2 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P47811, mitogen-activated protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5 to 20% PEG 4000, 100mM Na Citrate, 5mM DTT, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 29, 2004 / Details: SGX-CAT
RadiationMonochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→26.8 Å / Num. all: 23258 / Num. obs: 22784 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.115 / Χ2: 0.9 / Net I/σ(I): 8.8 / Scaling rejects: 19252
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.74 % / Mean I/σ(I) obs: 2.1 / Num. measured all: 12295 / Num. unique all: 1924 / Rsym value: 0.59 / Χ2: 1.07 / % possible all: 84.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNSrefinement
PDB_EXTRACT2data extraction
SGX-CATdata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.8 Å / FOM work R set: 0.721 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1110 4.8 %RANDOM
Rwork0.239 ---
all-23258 --
obs-22770 97.7 %-
Displacement parametersBiso mean: 72.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.7→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 0 60 5500
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.740.472420.433806848
2.74-2.790.405420.42847889
2.79-2.840.488530.426888941
2.84-2.890.618400.4359801020
2.89-2.940.441470.4059731020
2.94-30.468460.389861032
3-3.070.406580.3619851043
3.07-3.140.384430.3429771020
3.14-3.220.377430.29910161059
3.22-3.30.338490.2769821031
3.3-3.40.325430.2559911034
3.4-3.510.302530.27710141067
3.51-3.640.316620.2449721034
3.64-3.780.29500.22910131063
3.78-3.950.279490.21410041053
3.95-4.160.28670.2119901057
4.16-4.420.24510.19110071058
4.42-4.770.278560.19310121068
4.77-5.250.262450.20510351080
5.25-60.232460.22810541100
6-7.570.283690.20510441113
7.57-500.010.244560.19510841140
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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