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Yorodumi- PDB-2rf9: Crystal structure of the complex between the EGFR kinase domain a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rf9 | ||||||
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Title | Crystal structure of the complex between the EGFR kinase domain and a Mig6 peptide | ||||||
Components |
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Keywords | TRANSFERASE / kinase domain / inhibition / dimer / Alternative splicing / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphorylation / Polymorphism / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase / Ubl conjugation / Cytoplasm | ||||||
Function / homology | Function and homology information response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / lung vasculature development / lung epithelium development / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / bile acid biosynthetic process ...response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / lung vasculature development / lung epithelium development / regulation of keratinocyte differentiation / chondrocyte proliferation / negative regulation of protein autophosphorylation / bile acid biosynthetic process / skin morphogenesis / tissue homeostasis / cartilage development / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / fat pad development / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of nitric-oxide synthase activity / ERBB2 Activates PTK6 Signaling / morphogenesis of an epithelial fold / intracellular vesicle / lung alveolus development / Signaling by EGFR / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / eyelid development in camera-type eye / cerebral cortex cell migration / progesterone receptor signaling pathway / ERBB2 Regulates Cell Motility / regulation of JNK cascade / activation of phospholipase C activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of nitric oxide mediated signal transduction / salivary gland morphogenesis / regulation of peptidyl-tyrosine phosphorylation / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of phosphorylation / positive regulation of vasoconstriction / embryo implantation / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / cholesterol metabolic process / positive regulation of DNA repair / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / GTPase activator activity / neurogenesis / cellular response to dexamethasone stimulus / SHC1 events in ERBB2 signaling / ossification / positive regulation of synaptic transmission, glutamatergic / basal plasma membrane / regulation of ERK1 and ERK2 cascade / cholesterol homeostasis / neuron projection morphogenesis / positive regulation of superoxide anion generation / response to progesterone / liver development / positive regulation of DNA replication / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Signal transduction by L1 / epithelial cell proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Zhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Inhibition of the EGF receptor by binding of MIG6 to an activating kinase domain interface. Authors: Zhang, X. / Pickin, K.A. / Bose, R. / Jura, N. / Cole, P.A. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rf9.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rf9.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 2rf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/2rf9 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/2rf9 | HTTPS FTP |
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-Related structure data
Related structure data | 2rfdC 2rfeC 2gs7S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37563.457 Da / Num. of mol.: 2 / Fragment: Protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Plasmid: pFASTBAC-HT / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: P00533, receptor protein-tyrosine kinase #2: Protein | Mass: 6866.682 Da / Num. of mol.: 2 / Fragment: sequence database residues, 315-374 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERRFI1, MIG6 / Plasmid: pGEX6p1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJM3 |
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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: 42.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG3350, 300 mM KAC, 10% Glycerol and 100 mM NaAc, pH 5.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 9081 / % possible obs: 91.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.147 / Χ2: 1.049 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.5→3.63 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / Num. unique all: 736 / Χ2: 0.935 / % possible all: 74.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GS7 Resolution: 3.5→47.11 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 67.047 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.346 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→47.11 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: protein_rep.param |