+Open data
-Basic information
Entry | Database: PDB / ID: 4n0s | ||||||
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Title | Complex of ERK2 with caffeic acid | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | TRANSFERASE / caffeic acid complex / mitogen-activated protein kinase / signal-regulated kinase | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7992 Å | ||||||
Authors | Kurinov, I. / Malakhova, M. | ||||||
Citation | Journal: Cancer Prev Res (Phila) / Year: 2014 Title: Caffeic Acid Directly Targets ERK1/2 to Attenuate Solar UV-Induced Skin Carcinogenesis. Authors: Yang, G. / Fu, Y. / Malakhova, M. / Kurinov, I. / Zhu, F. / Yao, K. / Li, H. / Chen, H. / Li, W. / Lim, D.Y. / Sheng, Y. / Bode, A.M. / Dong, Z. / Dong, Z. #1: Journal: Cancer Res. / Year: 2012 Title: Norathyriol suppresses skin cancers induced by solar ultraviolet radiation by targeting ERK kinases. Authors: Li, J. / Malakhova, M. / Mottamal, M. / Reddy, K. / Kurinov, I. / Carper, A. / Langfald, A. / Oi, N. / Kim, M.O. / Zhu, F. / Sosa, C.P. / Zhou, K. / Bode, A.M. / Dong, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n0s.cif.gz | 231.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n0s.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 4n0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0s ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0s | HTTPS FTP |
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-Related structure data
Related structure data | 3sa0S S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41749.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL References: UniProt: P28482, mitogen-activated protein kinase |
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-Non-polymers , 5 types, 409 molecules
#2: Chemical | ChemComp-DHC / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.1 M - 1.4 M ammonium sulfate, 2% PEG 500 MME, 0.1 M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: DOUBLE-CRYSTALS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.7992→40 Å / Num. all: 35294 / Num. obs: 34906 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 34.3 | |||||||||||||||
Reflection shell | Resolution: 1.7992→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.1 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SA0 Resolution: 1.7992→36.862 Å / SU ML: 0.19 / σ(F): 1.39 / Phase error: 18.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7992→36.862 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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