+Open data
-Basic information
Entry | Database: PDB / ID: 4erk | ||||||
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Title | THE COMPLEX STRUCTURE OF THE MAP KINASE ERK2/OLOMOUCINE | ||||||
Components | EXTRACELLULAR REGULATED KINASE 2 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MAP KINASE / ERK2 | ||||||
Function / homology | Function and homology information phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Transcriptional and post-translational regulation of MITF-M expression and activity / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / diadenosine tetraphosphate biosynthetic process / Recycling pathway of L1 / neural crest cell development / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / Thrombin signalling through proteinase activated receptors (PARs) / regulation of Golgi inheritance / RAF/MAP kinase cascade / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / ERBB2-ERBB3 signaling pathway / lung morphogenesis / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of telomere capping / Bergmann glial cell differentiation / thyroid gland development / negative regulation of cell differentiation / decidualization / steroid hormone receptor signaling pathway / cellular response to cadmium ion / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / stress-activated MAPK cascade / positive regulation of cardiac muscle cell proliferation / lipopolysaccharide-mediated signaling pathway / sensory perception of pain / positive regulation of telomere maintenance via telomerase / ERK1 and ERK2 cascade / myelination / dendrite cytoplasm / phosphotyrosine residue binding / cellular response to amino acid starvation / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, Z. / Canagarajah, B. / Boehm, J.C. / Cobb, M.H. / Young, P.R. / Abdel-Meguid, S. / Adams, J.L. / Goldsmith, E.J. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structural basis of inhibitor selectivity in MAP kinases. Authors: Wang, Z. / Canagarajah, B.J. / Boehm, J.C. / Kassisa, S. / Cobb, M.H. / Young, P.R. / Abdel-Meguid, S. / Adams, J.L. / Goldsmith, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4erk.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4erk.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 4erk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4erk_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 4erk_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 4erk_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 4erk_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4erk ftp://data.pdbj.org/pub/pdb/validation_reports/er/4erk | HTTPS FTP |
-Related structure data
Related structure data | 1a9uC 1bl6C 1bl7C 1bmkC 3erkC 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: 42159.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: NPT7-HIS6 / Species (production host): Escherichia coli / Gene (production host): ERK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P63086, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-OLO / |
#4: 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: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.1 / Details: pH 6.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusionDetails: Wang, Z., (1997) Proc. Natl. Acad. Sci. USA, 94, 2327. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 21746 / % possible obs: 83.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.034 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.371 / % possible all: 77 |
Reflection | *PLUS Num. obs: 26042 / Num. measured all: 99305 / Rmerge(I) obs: 0.042 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ERK 1erk Resolution: 2.2→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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