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- PDB-4s2z: ERK2 Intrinsically active mutant R65S -

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Basic information

Entry
Database: PDB / ID: 4s2z
TitleERK2 Intrinsically active mutant R65S
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / signal transduction / phosphorylation / kinase
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 / 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 / Oxidative Stress Induced Senescence / 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 / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / cellular response to methionine / cellular response to toxic substance / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / RAF/MAP kinase cascade / mitogen-activated protein kinase kinase kinase binding / response to alcohol / ERBB signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / steroid hormone receptor signaling pathway / cellular response to insulin-like growth factor stimulus / androgen receptor signaling pathway / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / response to testosterone / regulation of cytoskeleton organization / response to exogenous dsRNA / pseudopodium / lung morphogenesis / face development / positive regulation of telomere maintenance / Bergmann glial cell differentiation / decidualization / thyroid gland development / peptidyl-threonine phosphorylation / progesterone receptor signaling pathway / regulation of ossification / MAP kinase activity / negative regulation of cell differentiation / mitogen-activated protein kinase / phosphatase binding / estrous cycle / Schwann cell development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / cellular response to platelet-derived growth factor stimulus / ERK1 and ERK2 cascade / phosphotyrosine residue binding / myelination / sensory perception of pain / RNA polymerase II CTD heptapeptide repeat kinase activity / dendrite cytoplasm / insulin-like growth factor receptor signaling pathway / cellular response to amino acid starvation / lipopolysaccharide-mediated signaling pathway
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / 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
Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLivnah, O. / Karamansha, Y.
CitationJournal: To be Published
Title: Multiple mechanisms render Erk proteins MEK-independent
Authors: Livnah, O. / Karamansha, Y.
History
DepositionJan 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1


Theoretical massNumber of molelcules
Total (without water)41,2601
Polymers41,2601
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.853, 70.051, 60.962
Angle α, β, γ (deg.)90.00, 109.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41260.438 Da / Num. of mol.: 1 / Mutation: R65S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mapk1, Erk2, Mapk, Prkm1 / Production host: Escherichia coli (E. coli)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 61 mM Ammonium Sulfate, 100mM Bis Tris pH 7.0, 12-15% (v/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2008
RadiationMonochromator: optical hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.48→1.5 Å / Num. all: 115054 / Num. obs: 62605 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERK

1erk
PDB Unreleased entry


Resolution: 1.48→45.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.585 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22051 3093 5.1 %RANDOM
Rwork0.19338 ---
all0.1965 59040 --
obs0.19481 57804 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.05 Å2
2--0.03 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 0 324 3135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192879
X-RAY DIFFRACTIONr_bond_other_d0.0010.022770
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9723904
X-RAY DIFFRACTIONr_angle_other_deg0.84636384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9724.275138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15415509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1731516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
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_it2.3683.231382
X-RAY DIFFRACTIONr_mcbond_other2.3683.2281381
X-RAY DIFFRACTIONr_mcangle_it3.3654.8371724
X-RAY DIFFRACTIONr_mcangle_other3.3644.8391725
X-RAY DIFFRACTIONr_scbond_it3.1823.5811497
X-RAY DIFFRACTIONr_scbond_other3.1813.5821498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9175.2352181
X-RAY DIFFRACTIONr_long_range_B_refined6.94727.2033615
X-RAY DIFFRACTIONr_long_range_B_other6.79326.6483459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 174 -
Rwork0.313 3187 -
obs--71.01 %

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