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- PDB-4fuy: Crystal Structure of the ERK2 complexed with EK2 -

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Basic information

Entry
Database: PDB / ID: 4fuy
TitleCrystal Structure of the ERK2 complexed with EK2
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated ...phospho-PLA2 pathway / Signaling by MAPK mutants / Suppression of apoptosis / RAF-independent MAPK1/3 activation / Signaling by Activin / Gastrin-CREB signalling pathway via PKC and MAPK / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / ERKs are inactivated / response to epidermal growth factor / Signaling by MAP2K mutants / Signaling by NODAL / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / regulation of cellular pH / positive regulation of macrophage proliferation / outer ear morphogenesis / Regulation of the apoptosome activity / regulation of Golgi inheritance / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of cytoskeleton organization / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / face development / Activation of the AP-1 family of transcription factors / androgen receptor signaling pathway / ERK/MAPK targets / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / pseudopodium / progesterone receptor signaling pathway / positive regulation of telomere capping / MAPK1 (ERK2) activation / negative regulation of cell differentiation / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone mediated signaling pathway / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / MAP kinase activity / phosphatase binding / mitogen-activated protein kinase / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / stress-activated MAPK cascade / Schwann cell development / Growth hormone receptor signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of telomerase activity / ERK1 and ERK2 cascade / cellular response to cadmium ion / cellular response to amino acid starvation / positive regulation of telomere maintenance via telomerase / myelination / NPAS4 regulates expression of target genes / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / response to nicotine / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / long-term synaptic potentiation / caveola / Negative regulation of FGFR3 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / B cell receptor signaling pathway / Spry regulation of FGF signaling / peptidyl-threonine phosphorylation / Signaling by high-kinase activity BRAF mutants / regulation of protein stability / MAP2K and MAPK activation / Oncogene Induced Senescence / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation
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-EK2 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, Y.N. / Stuckey, J.A. / Xie, X.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the ERK2 complexed with EK2
Authors: Kang, Y.N. / Stuckey, J.A. / Xie, X.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Structure summary

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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)42,3185
Polymers41,6731
Non-polymers6454
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 70.110, 60.670
Angle α, β, γ (deg.)90.000, 109.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 41673.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: ERK2, MAPK1, PRKM1, PRKM2 / Plasmid: pT7Blue / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase
#2: Chemical ChemComp-EK2 / {4-[4-(3,5-dichlorophenyl)-1H-pyrazol-5-yl]-1H-pyrrol-2-yl}(morpholin-4-yl)methanone


Mass: 391.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16Cl2N4O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM MES buffer, pH 6.5, 26-28% PEG-MME 2000, 200 mM ammonium sulfate and 20 mM 2-mercaptoethanol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→55 Å / Num. obs: 25073 / % possible obs: 95 % / Rmerge(I) obs: 0.045 / Χ2: 1.113 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.060.22518351.432184.2
2.06-2.130.17820621.374193.3
2.13-2.20.14720381.379194
2.2-2.290.12420621.384194.4
2.29-2.390.10320871.379194.9
2.39-2.520.08520791.299194.8
2.52-2.680.0720951.198196
2.68-2.880.05621251.084196.2
2.88-3.170.04521270.958197
3.17-3.630.03521500.799197.8
3.63-4.580.0321750.646198.1
4.58-550.02422380.549198.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.49 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9139 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1259 5.03 %RANDOM
Rwork0.1887 ---
obs0.1902 25013 95.53 %-
Displacement parametersBiso max: 129.09 Å2 / Biso mean: 32.2511 Å2 / Biso min: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.0886 Å20 Å22.569 Å2
2---5.226 Å20 Å2
3---3.1374 Å2
Refine analyzeLuzzati coordinate error obs: 0.216 Å
Refinement stepCycle: LAST / Resolution: 2→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 40 202 2926
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1300SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2836HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3467SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2836HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3861HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion2.9
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2126 121 4.55 %
Rwork0.1874 2538 -
all0.1886 2659 -
obs--95.53 %
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)
1-0.13620.23840.82090.23790.35411.51290.0020.00070.00670.00990.0146-0.0057-0.01470.0235-0.01660.01090.0322-0.04750.0464-0.0806-0.068624.05838.220325.0687
2-0.065-0.20910.11540.01670.02950.2935-0.0031-0.0140.00340.0049-0.0069-0.00050.00230.00130.01010.02520.0445-0.02840.0338-0.0244-0.06588.8933-3.657721.5059
30.5480.05020.29640.60420.0790.9523-0.0141-0.07020.01080.07440.0447-0.05710.01780.0496-0.0306-0.02610.007-0.0054-0.0387-0.01960.001616.4787-0.448911.9665
40.0409-0.0132-0.00210.0614-0.1622-0.0014-0.0009-0.00160.001-0.00010.00410.00210.0021-0.0045-0.0032-0.0218-0.02450.0151-0.00080.03790.0242-4.861-6.93612.7844
52.3206-0.98910.25950.34170.20650.30310.00430.06150.0594-0.02510.0020.01350.0188-0.0423-0.0062-0.0287-0.0066-0.0004-0.05440.01480.0055-0.62021.5477-4.0001
60.018-0.87960.11780.7588-0.28870.13480.0077-0.0064-0.02140.00860.00850.0021-0.0011-0.0054-0.0162-0.01670.0280.03-0.023-0.00810.036212.3447-15.22017.8572
7-0.0402-0.08460.00490.08170.01790.30760.0021-0.0025-0.00490.00940.00390.00420.0069-0.0101-0.0060.0304-0.0062-0.04270.0116-0.0256-0.040610.1032-1.739934.1383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - 63}A9 - 63
2X-RAY DIFFRACTION2{A|64 - 77}A64 - 77
3X-RAY DIFFRACTION3{A|78 - 169}A78 - 169
4X-RAY DIFFRACTION4{A|170 - 175}A170 - 175
5X-RAY DIFFRACTION5{A|176 - 311}A176 - 311
6X-RAY DIFFRACTION6{A|312 - 329}A312 - 329
7X-RAY DIFFRACTION7{A|337 - 356}A337 - 356

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