+Open data
-Basic information
Entry | Database: PDB / ID: 2zoq | ||||||
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Title | Structural dissection of human mitogen-activated kinase ERK1 | ||||||
Components | Mitogen-activated protein kinase 3 | ||||||
Keywords | TRANSFERASE / serine/threonine kinase / ERK1 / Acetylation / ATP-binding / Cell cycle / Host-virus interaction / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information positive regulation of xenophagy / xenophagy / 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 / ERKs are inactivated / response to epidermal growth factor ...positive regulation of xenophagy / xenophagy / 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 / 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 cyclase activity / positive regulation of macrophage proliferation / Regulation of the apoptosome activity / outer ear morphogenesis / cartilage development / regulation of cellular pH / regulation of Golgi inheritance / interleukin-1-mediated signaling pathway / 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 / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / MAPK3 (ERK1) activation / face development / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / pseudopodium / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate NADPH Oxidases / Regulation of HSF1-mediated heat shock response / MAP kinase activity / regulation of ossification / RHO GTPases Activate WASPs and WAVEs / phosphatase binding / mitogen-activated protein kinase / signal transduction in response to DNA damage / Signal attenuation / BMP signaling pathway / Nuclear events stimulated by ALK signaling in cancer / Schwann cell development / Growth hormone receptor signaling / peptidyl-tyrosine autophosphorylation / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / sensory perception of pain / : / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / NPAS4 regulates expression of target genes / ERK1 and ERK2 cascade / myelination / cellular response to amino acid starvation / RNA Polymerase I Promoter Opening / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / Regulation of PTEN gene transcription / Signal transduction by L1 / 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 / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / modulation of chemical synaptic transmission / Oncogene Induced Senescence / ISG15 antiviral mechanism / Regulation of actin dynamics for phagocytic cup formation / cellular response to reactive oxygen species / cellular response to mechanical stimulus / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Kinoshita, T. / Tada, T. / Nakae, S. / Yoshida, I. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Crystal structure of human mono-phosphorylated ERK1 at Tyr204 Authors: Kinoshita, T. / Yoshida, I. / Nakae, S. / Okita, K. / Gouda, M. / Matsubara, M. / Yokota, K. / Ishiguro, H. / Tada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zoq.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zoq.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zoq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2zoq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2zoq_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 2zoq_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/2zoq ftp://data.pdbj.org/pub/pdb/validation_reports/zo/2zoq | HTTPS FTP |
-Related structure data
Related structure data | 1erk S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43527.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK3, ERK1, PRKM3 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P27361, mitogen-activated protein kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2M ammonium sulphate, 2% polyethyleneglycol400, 0.1M, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→50 Å / Num. all: 28758 / Num. obs: 28700 / % possible obs: 99.8 % / Observed criterion σ(I): 144275 / Redundancy: 5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 23.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ERK 1erk Resolution: 2.39→45.57 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.39→45.57 Å
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Refine LS restraints |
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