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- PDB-6rfo: ERK2 MAP kinase with the activation loop of p38alpha -

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Basic information

Entry
Database: PDB / ID: 6rfo
TitleERK2 MAP kinase with the activation loop of p38alpha
ComponentsMitogen-activated protein kinase 1,Mitogen-activated protein kinase 14,Mitogen-activated protein kinase 1
KeywordsTRANSFERASE / NleD / effectors / T3SS / MAP kinase / phosphorylation
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / IFNG signaling activates MAPKs / Golgi Cisternae Pericentriolar Stack Reorganization / RHO GTPases Activate WASPs and WAVEs / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of actin dynamics for phagocytic cup formation / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signaling by Activin / Negative regulation of FGFR2 signaling / Signal transduction by L1 / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / diadenosine tetraphosphate biosynthetic process / MAP2K and MAPK activation / neural crest cell development / Recycling pathway of L1 / cellular response to toxic substance / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / cellular response to methionine / mitogen-activated protein kinase kinase kinase binding / response to epidermal growth factor / stress-activated protein kinase signaling cascade / positive regulation of cyclase activity / positive regulation of macrophage proliferation / response to alcohol / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / labyrinthine layer blood vessel development / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / RAF/MAP kinase cascade / Thrombin signalling through proteinase activated receptors (PARs) / ERBB signaling pathway / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / Neutrophil degranulation / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / positive regulation of myoblast fusion / KSRP (KHSRP) binds and destabilizes mRNA / cartilage condensation / cellular response to UV-B / regulation of stress-activated MAPK cascade / cellular response to insulin-like growth factor stimulus / positive regulation of muscle cell differentiation / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / Myogenesis / positive regulation of myotube differentiation / NFAT protein binding / ERBB2-ERBB3 signaling pathway / positive regulation of macrophage chemotaxis / regulation of cytokine production involved in inflammatory response / D-glucose import / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / p38MAPK cascade / response to exogenous dsRNA / Regulation of MITF-M-dependent genes involved in pigmentation / face development / positive regulation of telomere maintenance / lung morphogenesis / fatty acid oxidation / response to testosterone / MAP kinase kinase activity / cellular response to lipoteichoic acid
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitogen-activated protein kinase 1 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLivnah, O. / Eitan-Wexler, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1422/16 Israel
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial metalloprotease NleD selectively cleaves mitogen-activated protein kinases that have high flexibility in their activation loop.
Authors: Gur-Arie, L. / Eitan-Wexler, M. / Weinberger, N. / Rosenshine, I. / Livnah, O.
History
DepositionApr 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
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 1,Mitogen-activated protein kinase 14,Mitogen-activated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)42,8621
Polymers42,8621
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.999, 68.688, 60.231
Angle α, β, γ (deg.)90.00, 109.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase 1,Mitogen-activated protein kinase 14,Mitogen-activated protein kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK ...MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAPK 2 / 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 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAPK 2


Mass: 42862.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human)
Gene: Mapk1, Erk2, Mapk, Prkm1, MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
Production host: Escherichia coli (E. coli)
References: UniProt: P63086, UniProt: Q16539, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium sulfate, 0.1 M Bis-tris pH 6.8 or 6.5, 2% (w/v) PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.7→45.39 Å / Num. obs: 40460 / % possible obs: 99.4 % / Redundancy: 4 % / Rsym value: 0.062 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2160 / Rsym value: 0.716

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S31

4s31


Resolution: 1.7→45.39 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.025 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21874 2040 5 %RANDOM
Rwork0.1563 ---
obs0.15969 38401 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-1.79 Å2
2--1.93 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 0 173 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132647
X-RAY DIFFRACTIONr_bond_other_d0.0060.0172510
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.6433581
X-RAY DIFFRACTIONr_angle_other_deg1.4651.5775830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08922.361144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31115480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.5141517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022869
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02538
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.93.4131258
X-RAY DIFFRACTIONr_mcbond_other5.9043.4051256
X-RAY DIFFRACTIONr_mcangle_it6.9525.0931562
X-RAY DIFFRACTIONr_mcangle_other6.9515.0941562
X-RAY DIFFRACTIONr_scbond_it7.4794.0841389
X-RAY DIFFRACTIONr_scbond_other7.4764.0881390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5985.8812020
X-RAY DIFFRACTIONr_long_range_B_refined8.78240.6993032
X-RAY DIFFRACTIONr_long_range_B_other8.75940.3542999
X-RAY DIFFRACTIONr_rigid_bond_restr5.34735157
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 140 -
Rwork0.289 2819 -
obs--99.6 %

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