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Yorodumi- PDB-8u8k: Co-crystal structure of phosphorylated ERK2 in complex with ERK1/... -
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-Basic information
Entry | Database: PDB / ID: 8u8k | ||||||
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Title | Co-crystal structure of phosphorylated ERK2 in complex with ERK1/2 inhibitor #8 | ||||||
Components | Mitogen-activated protein kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE/INHIBITOR / protein kinase / ATP-competitive Inhibitor / conformation selection / TRANSFERASE-INHIBITOR complex | ||||||
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 / ERKs are inactivated / cytosine metabolic process ...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 / 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 / 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 / face development / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / progesterone receptor signaling pathway / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / pseudopodium / Recycling pathway of L1 / MAPK1 (ERK2) activation / Bergmann glial cell differentiation / negative regulation of 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 / phosphatase binding / mitogen-activated protein kinase / 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 / cellular response to amino acid starvation / 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 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Anderson, J.W. / Vigers, G.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2024 Title: Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2. Authors: Anderson, J.W. / Vaisar, D. / Jones, D.N. / Pegram, L.M. / Vigers, G.P. / Chen, H. / Moffat, J.G. / Ahn, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u8k.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u8k.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 8u8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u8k_validation.pdf.gz | 746.6 KB | Display | wwPDB validaton report |
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Full document | 8u8k_full_validation.pdf.gz | 748.5 KB | Display | |
Data in XML | 8u8k_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 8u8k_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/8u8k ftp://data.pdbj.org/pub/pdb/validation_reports/u8/8u8k | HTTPS FTP |
-Related structure data
Related structure data | 8u8jC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41134.031 Da / Num. of mol.: 1 / Mutation: A5S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P28482, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-W8U / ( Mass: 421.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClN7O / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Sequence details | The residue numbering in Uniprot P28482 is off by two relative to this residue numbering, such that ...The residue numbering in Uniprot P28482 is off by two relative to this residue numbering, such that Asp-167 in the Uniprot entry is Asp-165 in this entry. Also, the construct used in this structure determination lacks the MAAAAA at the amino-terminus, and has the following alanine substituted by a serine. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 32% PEG 3350, 0.1M Tris pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 29540 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.9 Å2 / Rpim(I) all: 0.06 / Rsym value: 0.146 / Net I/σ(I): 8.17 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4253 / Rpim(I) all: 0.132 / Rsym value: 0.032 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.3 Å / SU ML: 0.1997 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1772 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→21.3 Å
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Refine LS restraints |
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LS refinement shell |
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