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- PDB-1lez: CRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE... -

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Basic information

Entry
Database: PDB / ID: 1lez
TitleCRYSTAL STRUCTURE OF MAP KINASE P38 COMPLEXED TO THE DOCKING SITE ON ITS ACTIVATOR MKK3B
Components
  • MAP kinase kinase 3b
  • MITOGEN-ACTIVATED PROTEIN KINASE 14
KeywordsTRANSFERASE / PROTEIN-PEPTIDE COMPLEX / MAP KINASE / SERINE/THREONINE-PROTEIN KINASE / P38 / MKK3b
Function / homology
Function and homology information


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 / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence ...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 / Regulation of MITF-M-dependent genes involved in pigmentation / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Oxidative Stress Induced Senescence / ADP signalling through P2Y purinoceptor 1 / mitogen-activated protein kinase kinase / Regulation of TP53 Activity through Phosphorylation / Myogenesis / VEGFA-VEGFR2 Pathway / stress-activated protein kinase signaling cascade / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / positive regulation of myoblast fusion / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of myotube differentiation / NFAT protein binding / regulation of cytokine production involved in inflammatory response / D-glucose import / p38MAPK cascade / fatty acid oxidation / response to dietary excess / cellular response to lipoteichoic acid / response to muramyl dipeptide / MAP kinase kinase activity / MAP kinase activity / regulation of ossification / cellular response to vascular endothelial growth factor stimulus / positive regulation of blood vessel endothelial cell migration / mitogen-activated protein kinase / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / cardiac muscle contraction / positive regulation of brown fat cell differentiation / response to muscle stretch / striated muscle cell differentiation / Neutrophil degranulation / positive regulation of interleukin-12 production / regulation of cytokine production / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / DNA damage checkpoint signaling / placenta development / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import / cellular response to ionizing radiation / stem cell differentiation / negative regulation of canonical Wnt signaling pathway / response to insulin / bone development / cellular response to virus / positive regulation of protein import into nucleus / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / spindle pole / osteoblast differentiation / cellular response to tumor necrosis factor / kinase activity / MAPK cascade / cellular response to lipopolysaccharide / protein tyrosine kinase activity / angiogenesis / protein phosphatase binding / response to lipopolysaccharide / transcription by RNA polymerase II / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / nuclear speck / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / ATP binding / nucleus
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 3 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.-I. / Xu, B.-E. / Akella, R. / Cobb, M.H. / Goldsmith, E.J.
CitationJournal: Mol.Cell / Year: 2002
Title: Crystal structures of MAP kinase p38 complexed to the docking sites on its nuclear substrate MEF2A and activator MKK3b.
Authors: Chang, C.I. / Xu, B.E. / Akella, R. / Cobb, M.H. / Goldsmith, E.J.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Oct 27, 2021Group: Atomic model / Database references / Category: atom_site / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOGEN-ACTIVATED PROTEIN KINASE 14
B: MAP kinase kinase 3b


Theoretical massNumber of molelcules
Total (without water)43,4102
Polymers43,4102
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-9 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.353, 82.353, 123.266
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-396-

HOH

21A-450-

HOH

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Components

#1: Protein MITOGEN-ACTIVATED PROTEIN KINASE 14 / MAP KINASE P38 / Mitogen-activated protein kinase p38 / CRK1


Mass: 41338.160 Da / Num. of mol.: 1 / Mutation: M30N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: P38 / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P47811, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein/peptide MAP kinase kinase 3b / MKK3b


Mass: 2071.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: GenBank: 1778153, UniProt: O09110*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: PEG 8000, calcium acetate, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 289K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris-HCl1droppH7.4
2100 mM1dropNaCl
31 mMEDTA1drop
40.1 mMdithiothreitol1drop
58 mg/mlprotein1drop
620 %PEG80001reservoir
70.1 Msodium cacodylate1reservoirpH7.0
80.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 23, 2000 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.24→60 Å / Num. all: 29691 / Num. obs: 29661 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.24→2.29 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 60 Å / Num. obs: 22380
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→60 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 1882 RANDOM
Rwork0.216 --
all0.247 22048 -
obs0.236 18882 -
Refinement stepCycle: LAST / Resolution: 2.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2831 0 0 110 2941
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.74
Refinement
*PLUS
Lowest resolution: 60 Å / Num. reflection obs: 21231
Solvent computation
*PLUS
Displacement parameters
*PLUS

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