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- PDB-4gt3: ATP-bound form of the ERK2 kinase -

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Basic information

Entry
Database: PDB / ID: 4gt3
TitleATP-bound form of the ERK2 kinase
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / 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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsPozharski, E. / Zhang, J. / Shapiro, P.
CitationJournal: TO BE PUBLISHED
Title: ATP-bound form of the ERK2 kinase
Authors: Pozharski, E. / Zhang, J. / Shapiro, P.
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release

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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)43,1748
Polymers42,2361
Non-polymers9387
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.629, 69.259, 59.816
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP 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

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 0.1 M MES pH 6.5, 5% PEG400, 2M ammonium sulfate, sitting drop vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorDate: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.357→38.302 Å / Num. obs: 74850 / % possible obs: 92.6 % / Redundancy: 3.5 % / Rsym value: 0.055 / Net I/σ(I): 8.4
Reflection shellResolution: 1.357→1.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.269 / Num. measured all: 28600 / Num. unique all: 8625 / Rsym value: 0.26914 / % possible all: 73.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→38.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.2034 / WRfactor Rwork: 0.1666 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8712 / SU B: 4.331 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1 / SU Rfree: 0.0988 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 2071 5 %RANDOM
Rwork0.1663 ---
obs0.1681 41255 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.85 Å2 / Biso mean: 38.7387 Å2 / Biso min: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0.43 Å2
2--2.39 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.68→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 58 200 3037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193074
X-RAY DIFFRACTIONr_angle_refined_deg2.2921.9834204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7423.706143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5915511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2941520
X-RAY DIFFRACTIONr_chiral_restr0.1750.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212346
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 149 -
Rwork0.401 2895 -
all-3044 -
obs--96.33 %
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)
18.00131.7982-2.40658.29470.24910.1613-0.02370.41130.9507-0.25940.59070.3581-1.5542-0.9317-0.5670.34470.18430.00230.36740.13860.2162-11.292418.11671.0977
227.47881.192-11.21113.4983-2.01545.25530.3104-0.56181.03610.6870.0385-0.1351-0.45380.1893-0.34890.4604-0.01250.02030.175-0.0980.265-1.01320.0286.9963
39.94720.6599-4.4092.9947-2.32976.0291-0.1180.31410.23460.07320.38560.2697-0.5514-0.8125-0.26760.20990.0375-0.02570.2490.03460.1158-8.440512.13022.9876
44.99264.937-1.1813.6793-2.58727.7798-0.0097-0.08320.1490.3782-0.0714-0.4111-0.40030.63290.08110.1257-0.0551-0.07040.19740.02230.10559.548310.37514.5938
50.1501-0.32110.71060.8182-1.32094.297-0.0014-0.0306-0.0191-0.10170.09730.1039-0.0135-0.1683-0.09590.138-0.0053-0.02950.12340.02430.0971-2.36576.50863.5921
63.0138-0.47510.13652.18860.59321.9360.0507-0.02170.2721-0.097-0.0530.142-0.1739-0.24770.00220.03570.02740.00950.0365-0.00260.060.0556.150722.2607
75.10626.34963.178312.27745.76254.9041-0.38640.55210.0062-0.45250.4485-0.0256-0.30250.1529-0.0620.1599-0.00330.00410.2042-0.06010.181124.8669.435620.1202
83.41190.73510.78831.47320.22412.5389-0.03540.07110.5621-0.0178-0.0086-0.0607-0.28540.01740.04390.0616-0.00730.01650.0163-0.00640.160412.395712.813227.3849
97.39893.19411.13031.5473-0.27923.69560.1475-0.38720.20810.0277-0.19960.07010.18870.06090.05220.1821-0.005-0.01050.1198-0.00690.161921.87479.318437.5709
102.37191.81210.84931.75050.01351.41260.1853-0.32460.06680.1828-0.23830.0260.0111-0.1280.0530.0968-0.00770.00760.0834-0.03650.067415.5339.683538.3349
117.31882.7909-0.36242.18641.02531.82020.1138-0.0983-0.35180.26710.0214-0.3120.2018-0.0245-0.13520.085-0.0058-0.03860.04650.00980.07119.8111-2.438731.9614
124.20323.7132-0.38474.5057-0.25262.39250.020.0837-0.4229-0.0639-0.00990.0330.1447-0.1206-0.01010.03750.0318-0.0240.0607-0.01790.18460.5648-8.089722.8362
1313.9994-16.88263.269128.9177-14.755114.42620.6330.57410.0464-1.0963-0.8112-0.15580.60470.32030.17820.2788-0.01220.04850.4283-0.00920.293516.86932.2614.8617
149.21271.22970.40724.58960.52246.194-0.05790.0532-0.4061-0.35910.0598-0.24490.21150.5058-0.00190.12080.0037-0.02530.11830.01350.06155.80665.6694-5.0783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 30
2X-RAY DIFFRACTION2A31 - 38
3X-RAY DIFFRACTION3A39 - 59
4X-RAY DIFFRACTION4A60 - 71
5X-RAY DIFFRACTION5A72 - 107
6X-RAY DIFFRACTION6A108 - 174
7X-RAY DIFFRACTION7A175 - 185
8X-RAY DIFFRACTION8A186 - 236
9X-RAY DIFFRACTION9A237 - 252
10X-RAY DIFFRACTION10A253 - 294
11X-RAY DIFFRACTION11A295 - 310
12X-RAY DIFFRACTION12A311 - 328
13X-RAY DIFFRACTION13A329 - 334
14X-RAY DIFFRACTION14A335 - 356

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