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

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Basic information

Entry
Database: PDB / ID: 6flv
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 / Signal transduction by L1 / Negative regulation of FGFR2 signaling / 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 / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / 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 / RAF/MAP kinase cascade / regulation of cellular pH / Thrombin signalling through proteinase activated receptors (PARs) / regulation of Golgi inheritance / 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 / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / stress-activated MAPK cascade / cellular response to cAMP / positive regulation of telomere maintenance via telomerase / cellular response to epidermal growth factor stimulus / sensory perception of pain / phosphotyrosine residue binding / cellular response to cadmium ion / myelination / ERK1 and ERK2 cascade / 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. / : / 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. ...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-DTW / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
DepositionJan 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,1668
Polymers42,2361
Non-polymers9307
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-20 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.636, 69.599, 59.696
Angle α, β, γ (deg.)90.000, 108.770, 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


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


Mass: 425.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N10O4S
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.26 Å3/Da / Density % sol: 45.69 % / Mosaicity: 0.3 °
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: ID14-4 / Wavelength: 0.97631 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 1.91→46.05 Å / Num. obs: 28818 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.88 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.055 / Rrim(I) all: 0.106 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.982.80.65124820.7350.4530.79986.7
7.4-46.053.50.075220.990.0440.08397.9

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Processing

Software
NameVersionClassification
SCALA0.1.17data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYZ

3qyz


Resolution: 1.91→46.05 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.2188 1464 5.09 %
Rwork0.192 --
obs0.1934 28785 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 34.7273 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 1.91→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 55 200 3053
Biso mean--53.17 40.63 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9101-1.97830.30931230.26812402252586
1.9783-2.05750.27261610.23382682284397
2.0575-2.15120.23341260.21312744287099
2.1512-2.26460.25331670.204527702937100
2.2646-2.40650.25611430.195627692912100
2.4065-2.59220.21691430.201627832926100
2.5922-2.85310.2561310.197327922923100
2.8531-3.26580.21421670.186127662933100
3.2658-4.11420.1791350.166827912926100
4.1142-46.06330.19731680.18562822299099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41410.5712-0.5330.00250.30132.8861-0.06630.24270.3039-0.19490.18430.1874-0.5332-0.7826-0.09230.37460.06-0.07680.42760.09280.3027-13.804312.610533.8841
21.8180.92270.35181.05060.06411.27320.0301-0.04170.06610.0799-0.0166-0.0511-0.08360.0311-0.01130.15940.0235-0.01130.17460.00750.16751.28918.431556.9918
30.90540.7199-0.96712.904-3.9615.8051-0.02180.22520.0089-0.6791-0.0033-0.01520.69190.4920.00390.3251-0.02370.02090.3928-0.06180.2226-3.79490.925235.1493
40.52530.24630.11950.6140.00610.85490.0219-0.01940.0364-0.00290.01180.0011-0.0332-0.0541-0.05170.15040.0174-0.00850.27950.00260.1831-1.80117.380153.0632
54.99560.5194.74523.64880.98944.57690.2120.0711.0442-0.16510.2312-0.3071-0.9094-0.2621-0.41930.69320.0855-0.13290.5858-0.06840.5165-14.087915.67441.9327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 9:118)A9 - 118
2X-RAY DIFFRACTION2(chain A and resid 119:312)A119 - 312
3X-RAY DIFFRACTION3(chain A and resid 313:354)A313 - 354
4X-RAY DIFFRACTION4chain SS1 - 259
5X-RAY DIFFRACTION5chain BB1

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