+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+73 | ||||||
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Title | Crystal structure of human ERK2 mutant (Y36H) | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | TRANSFERASE / Kinase | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / 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 / RAF-independent MAPK1/3 activation / Suppression of apoptosis / 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 / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Signaling by LTK in cancer / 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 / regulation of stress-activated MAPK cascade / IFNG signaling activates MAPKs / Frs2-mediated activation / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / Activation of the AP-1 family of transcription factors / face development / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / : / positive regulation of telomere capping / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / RHO GTPases Activate NADPH Oxidases / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / mitogen-activated protein kinase / phosphatase binding / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / myelination / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / cellular response to amino acid starvation / RNA polymerase II CTD heptapeptide repeat kinase activity / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / Signal transduction by L1 / Regulation of PTEN gene transcription / caveola / long-term synaptic potentiation / Negative regulation of FGFR3 signaling / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / FCGR3A-mediated phagocytosis / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / B cell receptor signaling pathway / peptidyl-threonine phosphorylation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / response to nicotine / MAP2K and MAPK activation / regulation of protein stability / Oncogene Induced Senescence Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Park, Y.S. / Kim, M. / Ryu, S.E. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biodesign / Year: 2021 Title: Structural mechanism of inhibitor-resistance by ERK2 mutations Authors: Park, Y. / Kim, M. / Ryu, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e73.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e73.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e73 ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e73 | HTTPS FTP |
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-Related structure data
Related structure data | 7e75C 1erk S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.3 % / Description: plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100mM HEPES pH 7.0, 1.4M ammonium sulfate, 13% glycerol |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ERK 1erk 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→30.06 Å
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Refine LS restraints |
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LS refinement shell |
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