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- PDB-7e73: Crystal structure of human ERK2 mutant (Y36H) -

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Basic information

Entry
Database: PDB / ID: 7.0E+73
TitleCrystal structure of human ERK2 mutant (Y36H)
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


phospho-PLA2 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 / Signaling by MAP2K mutants ...phospho-PLA2 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 / Signaling by MAP2K mutants / Signaling by NODAL / response to epidermal growth factor / 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 / ERBB2-ERBB3 signaling pathway / positive regulation of macrophage chemotaxis / Activation of the AP-1 family of transcription factors / regulation of cytoskeleton organization / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / response to exogenous dsRNA / face development / MAPK1 (ERK2) activation / lung morphogenesis / positive regulation of telomere maintenance / Recycling pathway of L1 / Bergmann glial cell differentiation / thyroid gland development / androgen receptor signaling pathway / JUN kinase activity / steroid hormone receptor signaling pathway / Advanced glycosylation endproduct receptor signaling / RHO GTPases Activate NADPH Oxidases / peptidyl-threonine phosphorylation / negative regulation of cell differentiation / regulation of ossification / MAP kinase activity / 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 / Schwann cell development / Growth hormone receptor signaling / progesterone receptor signaling pathway / stress-activated MAPK cascade / Nuclear events stimulated by ALK signaling in cancer / ERK1 and ERK2 cascade / NPAS4 regulates expression of target genes / phosphotyrosine residue binding / myelination / Transcriptional and post-translational regulation of MITF-M expression and activity / NCAM signaling for neurite out-growth / 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 / lipopolysaccharide-mediated signaling pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / thymus development / Negative regulation of FGFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of PTEN gene transcription / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signal transduction by L1 / Spry regulation of FGF signaling / response to nicotine / B cell receptor signaling pathway / 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 / caveola / Regulation of actin dynamics for phagocytic cup formation / Negative regulation of MAPK pathway
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsPark, Y.S. / Kim, M. / Ryu, S.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biodesign / Year: 2021
Title: Structural mechanism of inhibitor-resistance by ERK2 mutations
Authors: Park, Y. / Kim, M. / Ryu, S.E.
History
DepositionFeb 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)41,7982
Polymers41,7021
Non-polymers961
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.857, 70.606, 60.905
Angle α, β, γ (deg.)90.000, 109.650, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 41701.902 Da / Num. of mol.: 1 / Mutation: Y36H
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.3 % / Description: plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM HEPES pH 7.0, 1.4M ammonium sulfate, 13% glycerol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.279→30.06 Å / Num. obs: 17017 / % possible obs: 94.92 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.07333 / Rpim(I) all: 0.04814 / Rrim(I) all: 0.08804 / Net I/σ(I): 10.95
Reflection shellResolution: 2.279→2.36 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.1736 / Mean I/σ(I) obs: 3.69 / Num. unique obs: 1505 / CC1/2: 0.914 / CC star: 0.977 / Rpim(I) all: 0.1315 / Rrim(I) all: 0.2189 / % possible all: 85.03

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000715data reduction
HKL-2000715data scaling
PHENIX1.16-3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERK

1erk
PDB Unreleased entry


Resolution: 2.28→30.06 Å / SU ML: 0.2583 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 22.6139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1709 10.04 %Random selection
Rwork0.1781 15307 --
obs0.1843 17016 94.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.96 Å2
Refinement stepCycle: LAST / Resolution: 2.28→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 5 102 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842905
X-RAY DIFFRACTIONf_angle_d0.93333937
X-RAY DIFFRACTIONf_chiral_restr0.0514432
X-RAY DIFFRACTIONf_plane_restr0.0054506
X-RAY DIFFRACTIONf_dihedral_angle_d3.2221765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.26361230.19831109X-RAY DIFFRACTION82.8
2.35-2.420.2521410.18731221X-RAY DIFFRACTION92.59
2.42-2.510.27771490.17691229X-RAY DIFFRACTION92.61
2.51-2.610.22221190.18091274X-RAY DIFFRACTION93.74
2.61-2.730.25041500.19391245X-RAY DIFFRACTION94.13
2.73-2.870.2681450.1961286X-RAY DIFFRACTION95.27
2.87-3.050.3071370.19661310X-RAY DIFFRACTION96.6
3.05-3.290.25241420.19281292X-RAY DIFFRACTION97.42
3.29-3.620.26551420.19371311X-RAY DIFFRACTION97.85
3.62-4.140.21861550.16741330X-RAY DIFFRACTION98.54
4.14-5.210.20191540.15121335X-RAY DIFFRACTION98.87
5.21-30.060.20871520.16471365X-RAY DIFFRACTION98.57

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