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

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Basic information

Entry
Database: PDB / ID: 6frp
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 / 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 / Schwann cell development / estrous cycle / 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
5'-azido-5'-deoxyadenosine / 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
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 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 2.0May 15, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 20, 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)43,0328
Polymers42,2361
Non-polymers7977
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-20 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.674, 70.029, 59.520
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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZAS / 5'-azido-5'-deoxyadenosine


Mass: 292.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
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: BM30A / Wavelength: 0.97968 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97968 Å / Relative weight: 1
ReflectionResolution: 1.53→23.072 Å / Num. all: 55458 / Num. obs: 55458 / % possible obs: 97.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.033 / Rrim(I) all: 0.049 / Rsym value: 0.035 / Net I/av σ(I): 6.5 / Net I/σ(I): 14.6 / Num. measured all: 118340
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
1.53-1.612.20.5011.41832881600.4830.7640.501198.3
1.61-1.712.20.2872.61730677350.2810.4430.2871.898.3
1.71-1.832.20.1724.21593872200.170.2660.172397.9
1.83-1.982.10.0917.81455367710.0950.1460.0915.997.8
1.98-2.162.10.04714.31279861510.0510.0760.04711.597.3
2.16-2.422.10.02824.71157355910.030.0450.02818.297.2
2.42-2.7920.02129.3991349050.0210.0310.02126.296.8
2.79-3.4220.01437.4810940570.0150.0220.01438.894.5
3.42-4.8420.01321.6626431510.0140.0210.01354.794.4
4.84-24.2252.10.0257.8355817170.0390.0560.02556.792.3

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Processing

Software
NameVersionClassification
SCALA3.2.19data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYZ

3qyz


Resolution: 1.53→23.072 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.91 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 4477 4.95 %
Rwork0.1611 85906 -
obs0.1635 55377 80.41 %
all-90383 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.81 Å2 / Biso mean: 30.5345 Å2 / Biso min: 13.75 Å2
Refinement stepCycle: final / Resolution: 1.53→23.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 47 348 3153
Biso mean--43.46 44.19 -
Num. residues----340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.54740.3991430.35222815295881
1.5474-1.56560.32531430.31872893303680
1.5656-1.58470.30691750.28692836301180
1.5847-1.60470.35051750.28062856303181
1.6047-1.62580.32981460.2752831297780
1.6258-1.64810.31081670.26092818298580
1.6481-1.67160.33241470.24612966311381
1.6716-1.69660.26231500.24052842299281
1.6966-1.72310.26721450.22512925307081
1.7231-1.75130.27921510.19942857300880
1.7513-1.78150.2521300.19362859298981
1.7815-1.81390.22661420.17912940308281
1.8139-1.84880.26181250.16992872299781
1.8488-1.88650.21851320.15882885301781
1.8865-1.92750.23131310.16952935306680
1.9275-1.97230.21241350.15592837297280
1.9723-2.02160.21811180.1472915303381
2.0216-2.07620.21261400.14192816295679
2.0762-2.13730.18261640.13612852301680
2.1373-2.20620.19491740.12982863303780
2.2062-2.2850.18231510.12922765291680
2.285-2.37640.21961760.13612846302280
2.3764-2.48440.21211550.13632801295679
2.4844-2.61520.20291760.14412818299480
2.6152-2.77880.19041660.14972869303581
2.7788-2.9930.21211460.15232879302581
2.993-3.29340.20881390.14472826296579
3.2934-3.76820.19671320.1382744287677
3.7682-4.74070.17021530.13842986313984
4.7407-23.07440.18591500.19062959310983

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