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- PDB-8zjv: Crystal Structure of the ERK2 complexed with 5-Iodotubercidin -

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Basic information

Entry
Database: PDB / ID: 8zjv
TitleCrystal Structure of the ERK2 complexed with 5-Iodotubercidin
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / Inhibitor
Function / homology
Function and homology information


phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process ...phospho-PLA2 pathway / interleukin-34-mediated signaling pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / Signaling by NODAL / Signaling by MAP2K mutants / ERKs are inactivated / RSK activation / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of the apoptosome activity / positive regulation of macrophage proliferation / regulation of cellular pH / outer ear morphogenesis / Signaling by LTK in cancer / regulation of Golgi inheritance / positive regulation of peptidyl-threonine phosphorylation / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / IFNG signaling activates MAPKs / regulation of stress-activated MAPK cascade / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / RUNX2 regulates osteoblast differentiation / ERK/MAPK targets / response to exogenous dsRNA / pseudopodium / MAPK1 (ERK2) activation / lung morphogenesis / face development / positive regulation of telomere maintenance / Recycling pathway of L1 / Bergmann glial cell differentiation / thyroid gland development / Advanced glycosylation endproduct receptor signaling / peptidyl-threonine phosphorylation / negative regulation of cell differentiation / regulation of ossification / MAP kinase activity / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / Regulation of HSF1-mediated heat shock response / mitogen-activated protein kinase / Signal attenuation / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Schwann cell development / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / phosphotyrosine residue binding / myelination / NCAM signaling for neurite out-growth / Transcriptional and post-translational regulation of MITF-M expression and activity / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / cellular response to amino acid starvation / Negative regulation of FGFR3 signaling / ESR-mediated signaling / Negative regulation of FGFR2 signaling / lipopolysaccharide-mediated signaling pathway / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / thymus development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of PTEN gene transcription / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signal transduction by L1 / B cell receptor signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / Oncogene Induced Senescence / FCERI mediated MAPK activation / positive regulation of cholesterol biosynthetic process / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / caveola / Negative regulation of MAPK pathway / epidermal growth factor receptor signaling pathway / long-term synaptic potentiation / Interferon gamma signaling
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
Similarity search - Domain/homology
Chem-5ID / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYang, Y. / Fu, L. / Chen, R. / Cheng, H. / Sun, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of the ERK2 complexed with 5-Iodotubercidin
Authors: Yang, Y. / Fu, L. / Chen, R. / Cheng, H. / Sun, X.
History
DepositionMay 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: 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)41,75710
Polymers40,7591
Non-polymers9989
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitogen-activated protein kinase 1
hetero molecules

A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51420
Polymers81,5182
Non-polymers1,99618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5610 Å2
ΔGint-118 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.979, 96.979, 95.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-409-

CL

21A-600-

HOH

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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: 40758.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13IN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium Sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→41.52 Å / Num. obs: 48367 / % possible obs: 99.66 % / Redundancy: 15.1 % / Biso Wilson estimate: 25.44 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1282 / Net I/σ(I): 16.67
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 15.5 % / Rmerge(I) obs: 2.026 / Num. unique obs: 4796 / CC1/2: 0.685 / CC star: 0.902 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AX3

5ax3


Resolution: 1.8→41.52 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 2417 5 %
Rwork0.19 45938 -
obs0.1915 48355 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 53 304 3207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642967
X-RAY DIFFRACTIONf_angle_d0.79784021
X-RAY DIFFRACTIONf_chiral_restr0.0503437
X-RAY DIFFRACTIONf_plane_restr0.0078511
X-RAY DIFFRACTIONf_dihedral_angle_d12.74321110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32111330.31262672X-RAY DIFFRACTION99.08
1.84-1.880.33141410.27092655X-RAY DIFFRACTION99.36
1.88-1.920.26871210.24332659X-RAY DIFFRACTION99.36
1.92-1.970.24741330.22182695X-RAY DIFFRACTION99.51
1.97-2.020.24781490.21922667X-RAY DIFFRACTION99.51
2.02-2.080.23371600.22632X-RAY DIFFRACTION99.29
2.08-2.150.22271400.20032676X-RAY DIFFRACTION99.68
2.15-2.220.2061730.20262670X-RAY DIFFRACTION99.61
2.23-2.310.21751090.20272699X-RAY DIFFRACTION99.82
2.31-2.420.21611480.20062697X-RAY DIFFRACTION99.82
2.42-2.550.20931330.19952705X-RAY DIFFRACTION99.86
2.55-2.710.22881310.20572722X-RAY DIFFRACTION99.93
2.71-2.920.2811400.19892721X-RAY DIFFRACTION100
2.92-3.210.24161910.19762662X-RAY DIFFRACTION99.96
3.21-3.670.20911620.17362740X-RAY DIFFRACTION100
3.68-4.630.18031190.15312780X-RAY DIFFRACTION100
4.63-41.520.18991340.17352886X-RAY DIFFRACTION99.7

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