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

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Basic information

Entry
Database: PDB / ID: 6fle
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 / IFNG signaling activates MAPKs ...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 / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / 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 / 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 / ESR-mediated signaling / Regulation of the apoptosome activity / Interferon gamma signaling / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / FCERI mediated MAPK activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / Neutrophil degranulation / trachea formation / regulation of cytoskeleton organization / regulation of early endosome to late endosome transport / cellular response to organic substance / regulation of stress-activated MAPK cascade / positive regulation of macrophage chemotaxis / response to exogenous dsRNA / lung morphogenesis / ERBB2-ERBB3 signaling pathway / face development / androgen receptor signaling pathway / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / decidualization / steroid hormone mediated signaling pathway / regulation of ossification / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / stress-activated MAPK cascade / Schwann cell development / sensory perception of pain / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / ERK1 and ERK2 cascade / cellular response to cadmium ion / positive regulation of telomere maintenance via telomerase / cellular response to amino acid starvation / myelination / dendrite cytoplasm / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / positive regulation of translation / thymus development / positive regulation of peptidyl-threonine phosphorylation / response to nicotine / long-term synaptic potentiation
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-DQ2 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 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

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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)42,8494
Polymers42,2361
Non-polymers6143
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 70.080, 59.650
Angle α, β, γ (deg.)90.000, 108.510, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DQ2 / [(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[3-(2-azanylethylamino)-3-oxidanylidene-propyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino-azanylidene-azanium


Mass: 439.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N10O4S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.48→38.571 Å / Num. obs: 59645 / % possible obs: 94.1 % / Redundancy: 5.609 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Χ2: 0.994 / Net I/σ(I): 18.99 / Num. measured all: 334576
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.48-1.525.5970.8022.0223974467142830.5250.88491.7
1.52-1.565.7050.6662.5624473453142900.7180.73394.7
1.56-1.615.7130.5423.2124167443642300.7830.59695.4
1.61-1.665.7020.4323.9923241427440760.8790.47695.4
1.66-1.715.6920.3375.0622740419339950.930.37195.3
1.71-1.775.6770.2716.3421777402738360.9580.29895.3
1.77-1.845.6540.2018.420924387637010.9740.22295.5
1.84-1.915.6290.15210.8420209375735900.9850.16795.6
1.91-25.5820.10714.5519315362034600.9920.11895.6
2-2.095.5830.07918.8718094342132410.9960.08794.7
2.09-2.215.5460.05923.8417176331130970.9980.06593.5
2.21-2.345.5090.04927.9215409305927970.9980.05491.4
2.34-2.55.4190.0432.7813282292924510.9990.04483.7
2.5-2.75.6290.03538.5412654273822480.9990.03882.1
2.7-2.965.720.03143.3813990248524460.9990.03498.4
2.96-3.315.6750.02749.7412728227322430.9990.0398.7
3.31-3.825.6320.02555.9711073199219660.9990.02898.7
3.82-4.685.5160.02458.219300170216860.9990.02699.1
4.68-6.625.3430.02757.437053133913200.9980.0398.6
6.62-38.5714.350.02852.6829977496890.9980.03392

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Processing

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

3qyz


Resolution: 1.48→38.571 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 2950 4.95 %
Rwork0.1539 56691 -
obs0.1558 59641 94.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.38 Å2 / Biso mean: 36.0822 Å2 / Biso min: 14.85 Å2
Refinement stepCycle: final / Resolution: 1.48→38.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 39 296 3104
Biso mean--63.13 44.4 -
Num. residues----341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4802-1.50450.29321310.23792568269991
1.5045-1.53040.27061310.21962713284494
1.5304-1.55830.24941440.20722714285895
1.5583-1.58820.23941340.1892707284195
1.5882-1.62070.2331400.17442725286595
1.6207-1.65590.2191430.15862717286095
1.6559-1.69440.21161360.14922721285795
1.6944-1.73680.21551600.14932720288096
1.7368-1.78380.20741450.14122695284096
1.7838-1.83620.21321560.13472725288195
1.8362-1.89550.21151340.13352756289096
1.8955-1.96320.16251420.12292748289096
1.9632-2.04190.17911520.12962692284495
2.0419-2.13480.17781410.12812730287195
2.1348-2.24730.19981410.13452644278593
2.2473-2.38810.2141520.13582575272790
2.3881-2.57240.21361160.14012253236978
2.5724-2.83120.18511310.1532677280893
2.8312-3.24080.19231450.15472862300799
3.2408-4.08230.17371320.15062877300999
4.0823-38.58440.18671440.17562872301697

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