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- PDB-6fi3: Crystal structure of ERK2 in complex with an adenosine derivative -

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Basic information

Entry
Database: PDB / ID: 6fi3
TitleCrystal structure of ERK2 in complex with an adenosine derivative
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN 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 / 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 / mitogen-activated protein kinase kinase kinase binding / cellular response to methionine / response to epidermal growth factor / positive regulation of macrophage proliferation / response to alcohol / regulation of cellular pH / outer ear morphogenesis / regulation of Golgi inheritance / labyrinthine layer blood vessel development / RAF/MAP kinase cascade / Thrombin signalling through proteinase activated receptors (PARs) / ERBB signaling pathway / Neutrophil degranulation / mammary gland epithelial cell proliferation / trachea formation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / cellular response to insulin-like growth factor stimulus / ERBB2-ERBB3 signaling pathway / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / response to exogenous dsRNA / face development / lung morphogenesis / positive regulation of telomere maintenance / response to testosterone / pseudopodium / Bergmann glial cell differentiation / androgen receptor signaling pathway / thyroid gland development / steroid hormone receptor signaling pathway / decidualization / MAP kinase activity / negative regulation of cell differentiation / regulation of ossification / JUN kinase activity / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / progesterone receptor signaling pathway / stress-activated MAPK cascade / estrous cycle / positive regulation of cardiac muscle cell proliferation / cellular response to platelet-derived growth factor stimulus / cellular response to cAMP / sensory perception of pain / dendrite cytoplasm / phosphotyrosine residue binding / myelination / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / ERK1 and ERK2 cascade / cellular response to epidermal growth factor stimulus
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
Chem-DJ2 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsGelin, M. / Labesse, G.
Funding support France, 1items
OrganizationGrant numberCountry
FRISBIANR-10-INSB-05 France
CitationJournal: To be published
Title: Crystal structure of ERK2 in complex with an adenosine derivative
Authors: Gelin, M. / Pochet, S. / Labesse, G.
History
DepositionJan 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8486
Polymers42,2361
Non-polymers6135
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-13 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.564, 69.957, 59.529
Angle α, β, γ (deg.)90.000, 108.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 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


Mass: 42235.547 Da / Num. of mol.: 1
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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DJ2 / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(azanyloxymethyl)oxolane-3,4-diol


Mass: 282.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.27 Å3/Da / Density % sol: 45.91 % / Mosaicity: 0.28 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 2000, 0.1M MES pH 6.5, 0.1M ammonium sulfate, 0.02M beta-mercaptoethanol, 0.002M magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97268 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97268 Å / Relative weight: 1
ReflectionResolution: 1.52→46.038 Å / Num. all: 55670 / Num. obs: 55670 / % possible obs: 96.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 21.76 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.059 / Rsym value: 0.047 / Net I/av σ(I): 7 / Net I/σ(I): 10.2 / Num. measured all: 133136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.52-1.572.40.5231.51326754750.4020.6630.5231.996.9
1.57-1.632.40.38421265453170.2980.4890.3842.596.7
1.63-1.72.30.2742.71137950450.2180.3520.2743.296.1
1.7-1.772.40.2013.61206349420.1570.2570.2014.597.7
1.77-1.862.40.1444.91153347240.1120.1830.144697.6
1.86-1.962.40.1027.11050744370.0810.1310.1027.996.9
1.96-2.082.30.0749.5956741610.0590.0950.07410.395.4
2.08-2.232.50.0611965539280.0460.0760.0613.296
2.23-2.42.40.05112.6885336390.040.0650.05115.295.4
2.4-2.632.30.04613.3747832710.0360.0590.04616.893.4
2.63-2.942.50.04115755930240.0310.0520.04119.594.8
2.94-3.42.50.0413.8662526910.0310.0510.0421.795.1
3.4-4.162.30.03714.7522022430.0290.0480.0372394.4
4.16-5.892.50.03616.3443717950.0280.0460.03624.196.5
5.89-46.0382.40.03613.323399780.0290.0470.03623.693

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYZ

3qyz


Resolution: 1.52→46.038 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 2841 5.11 %
Rwork0.1498 52806 -
obs0.1522 55647 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.51 Å2 / Biso mean: 32.3519 Å2 / Biso min: 13.79 Å2
Refinement stepCycle: final / Resolution: 1.52→46.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 37 332 3121
Biso mean--49.62 47.17 -
Num. residues----339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.54620.31981300.2472636276697
1.5462-1.57430.24091420.21492667280997
1.5743-1.60460.24371370.1942672280997
1.6046-1.63740.23231370.18052641277896
1.6374-1.6730.25061650.17562612277796
1.673-1.71190.20481320.16472629276196
1.7119-1.75470.22331340.1552697283197
1.7547-1.80220.22991620.14692681284398
1.8022-1.85520.20451390.14682663280297
1.8552-1.91510.21261640.13292635279997
1.9151-1.98350.18881430.12532637278095
1.9835-2.06290.1951290.12792625275495
2.0629-2.15680.19121170.12472660277796
2.1568-2.27050.17891430.12682611275495
2.2705-2.41280.17991480.13682643279195
2.4128-2.59910.2031210.14312581270293
2.5991-2.86060.20311590.14992597275695
2.8606-3.27440.18421480.1462608275694
3.2744-4.1250.16671410.13952622276394
4.125-46.05880.21481500.17322689283995

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