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

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Basic information

Entry
Database: PDB / ID: 6fxv
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 / RHO GTPases Activate WASPs and WAVEs / Transcriptional and post-translational regulation of MITF-M expression and activity ...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 / RHO GTPases Activate WASPs and WAVEs / 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 / Estrogen-stimulated signaling through PRKCZ / Regulation of actin dynamics for phagocytic cup formation / 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 / Signaling by Activin / 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 / 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 / Recycling pathway of L1 / neural crest cell development / response to alcohol / cellular response to toxic substance / cellular response to methionine / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / mitogen-activated protein kinase kinase kinase binding / cytosine metabolic process / response to epidermal growth factor / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / RAF/MAP kinase cascade / Thrombin signalling through proteinase activated receptors (PARs) / ERBB signaling pathway / labyrinthine layer blood vessel development / 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 / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / androgen receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / pseudopodium / response to testosterone / positive regulation of telomere capping / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / decidualization / steroid hormone receptor signaling pathway / MAP kinase activity / regulation of ossification / estrous cycle / mitogen-activated protein kinase / phosphatase binding / progesterone receptor signaling pathway / Schwann cell development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / cellular response to cAMP / sensory perception of pain / positive regulation of telomere maintenance via telomerase / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / myelination / ERK1 and ERK2 cascade / dendrite cytoplasm / cellular response to amino acid starvation
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
Chem-E9W / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGelin, M. / Labesse, G.
Funding support France, 1items
OrganizationGrant numberCountry
FRISBIANR-10-INSB-05 France
CitationJournal: To be published
Title: None
Authors: Gelin, M. / Pochet, S. / Labesse, G.
History
DepositionMar 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 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 / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0636
Polymers42,3121
Non-polymers7515
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.788, 70.583, 59.850
Angle α, β, γ (deg.)90.000, 109.020, 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: 42311.668 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-E9W / azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(prop-2-ynylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]azanium


Mass: 420.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N9O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.3 Å3/Da / Density % sol: 46.58 % / Mosaicity: 0.2 °
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: 1.00046 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00046 Å / Relative weight: 1
ReflectionResolution: 1.53→43.329 Å / Num. all: 51825 / Num. obs: 51825 / % possible obs: 89.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 22.89 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.074 / Rsym value: 0.058 / Net I/av σ(I): 4.8 / Net I/σ(I): 9.2 / Num. measured all: 127711
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
1.53-1.582.30.5461.3901439800.430.6980.5461.970.8
1.58-1.642.50.3991.91219449760.3050.5040.3992.691.4
1.64-1.712.50.2892.61202948620.2210.3660.2893.592.7
1.71-1.792.40.2083.51115946400.1620.2650.2084.592.3
1.79-1.872.40.1444.91077144220.1130.1840.144691.5
1.87-1.982.50.1066.71065441790.0830.1350.1067.991.7
1.98-2.12.50.0828985539670.0650.1060.0829.991.3
2.1-2.242.40.0679.2883736540.0540.0860.06711.789.8
2.24-2.422.60.0610.2902135070.0480.0780.0613.591.9
2.42-2.652.50.05411.5815332120.0430.0690.05414.891.8
2.65-2.962.50.05210.9717529270.0420.0670.05215.892.2
2.96-3.422.60.0511.4673526090.0390.0640.0517.892.9
3.42-4.192.40.0511.4530021920.040.0650.0518.192.4
4.19-5.932.60.05110.5454417530.040.0650.05118.994.4
5.93-43.3292.40.057822709450.0430.0720.05718.191.4

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Processing

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

3qyz


Resolution: 1.53→43.329 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.1932 2637 5.09 %
Rwork0.1524 --
obs0.1544 51802 89.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.14 Å2 / Biso mean: 32.7201 Å2 / Biso min: 15.03 Å2
Refinement stepCycle: final / Resolution: 1.53→43.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 46 340 3128
Biso mean--40.99 43.14 -
Num. residues----337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.55780.3066930.25081870196365
1.5578-1.58780.29121160.21382244236078
1.5878-1.62020.21331560.18582607276390
1.6202-1.65540.23241340.17112639277393
1.6554-1.6940.24461370.16832697283493
1.694-1.73630.22571360.16692654279092
1.7363-1.78330.22871380.16612652279092
1.7833-1.83570.21611450.15992580272590
1.8357-1.8950.22491540.14872672282693
1.895-1.96270.21961560.13882611276791
1.9627-2.04130.18651240.14132646277091
2.0413-2.13420.21611370.13772651278891
2.1342-2.24670.15411370.13132546268389
2.2467-2.38750.17881490.13272678282792
2.3875-2.57180.20171290.14262655278491
2.5718-2.83060.18971630.15172613277691
2.8306-3.240.2041530.15632704285793
3.24-4.08160.15381270.14472705283292
4.0816-43.34590.19461530.16492741289493

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