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- PDB-2y9q: Crystal structure of human ERK2 complexed with a MAPK docking peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y9q | ||||||
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Title | Crystal structure of human ERK2 complexed with a MAPK docking peptide | ||||||
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![]() | TRANSFERASE / SIGNALING / PROTEIN-PROTEIN INTERACTION | ||||||
Function / homology | ![]() phospho-PLA2 pathway / calcium-dependent protein serine/threonine kinase activity / 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 / ERKs are inactivated ...phospho-PLA2 pathway / calcium-dependent protein serine/threonine kinase activity / 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 / ERKs are inactivated / cytosine metabolic process / 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 / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Negative feedback regulation of MAPK pathway / calcium/calmodulin-dependent protein kinase activity / 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 / 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 / Recycling pathway of L1 / MAPK1 (ERK2) activation / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / Advanced glycosylation endproduct receptor signaling / steroid hormone receptor signaling pathway / 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 / 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 / cellular response to amino acid starvation / myelination / 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 / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / Signal transduction by L1 / caveola / long-term synaptic potentiation / 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 / peptidyl-threonine phosphorylation / B cell receptor signaling pathway / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barkai, T. / Garai, A. / Toeroe, I. / Remenyi, A. | ||||||
![]() | ![]() Title: Specificity of Linear Motifs that Bind to a Common Mitogen-Activated Protein Kinase Docking Groove. Authors: Garai, A. / Zeke, A. / Gogl, G. / Toro, I. / Fordos, F. / Blankenburg, H. / Barkai, T. / Varga, J. / Alexa, A. / Emig, D. / Albrecht, M. / Remenyi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.1 KB | Display | ![]() |
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PDB format | ![]() | 140.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.1 KB | Display | ![]() |
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Full document | ![]() | 838.2 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xrwC ![]() 2xs0C ![]() 2y8oC ![]() 3teiC ![]() 4fmqC ![]() 2gphS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41588.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Protein/peptide | Mass: 2044.516 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOCKING PEPTIDE, RESIDUES 434-451 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: Q9BUB5, non-specific serine/threonine protein kinase |
#3: Chemical | ChemComp-ANP / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 12% PEG 20000, 100 MM MIB BUFFER PH 6.5 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 25, 2010 / Details: DUAL SLITS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→53.86 Å / Num. obs: 59403 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 5.32 % / Biso Wilson estimate: 14.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.82 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.92 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GPH Resolution: 1.55→53.856 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 17.38 / Stereochemistry target values: ML Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS FOR REFINEMENT. RESIDUES FROM A-1 TO A8, A359, A360, AND B454 ARE DISORDERED. RESIDUES A79, A180, AND A314 ARE MODELLED WITH TRUNCATED SIDECHAINS.
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.593 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→53.856 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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