+Open data
-Basic information
Entry | Database: PDB / ID: 4r3r | ||||||
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Title | Crystal structures of EGFR in complex with Mig6 | ||||||
Components |
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Keywords | TRANSFERASE / Kinase / phophorylation / ATP hydrolysis / Mig6 / PHOSPHORYLATION | ||||||
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 / Resolution: 3.25 Å | ||||||
Authors | Park, E. / Kim, N. / Yi, Z. / Cho, A. / Kim, K. / Ficarro, S.B. / Park, A. / Park, W.Y. / Murray, B. / Meyerson, M. ...Park, E. / Kim, N. / Yi, Z. / Cho, A. / Kim, K. / Ficarro, S.B. / Park, A. / Park, W.Y. / Murray, B. / Meyerson, M. / Beroukim, R. / Marto, J.A. / Cho, J. / Eck, M.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6. Authors: Park, E. / Kim, N. / Ficarro, S.B. / Zhang, Y. / Lee, B.I. / Cho, A. / Kim, K. / Park, A.K. / Park, W.Y. / Murray, B. / Meyerson, M. / Beroukhim, R. / Marto, J.A. / Cho, J. / Eck, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r3r.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r3r.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/4r3r ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r3r | HTTPS FTP |
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-Related 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: 36937.742 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 696-1018) / Mutation: L858R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, Erbb1(EGFR), HER1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 References: UniProt: P00533, receptor protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1067.002 Da / Num. of mol.: 1 / Fragment: segment 2 (UNP residues 392-398) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UJM3 |
#3: 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: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40% PEG400, 0.15M SODIUM CHLORIDE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2012 | ||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.26→50 Å / Num. obs: 7110 / % possible obs: 87.75 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 82.7 Å2 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→45.755 Å / SU ML: 0.42 / σ(F): 1.36 / Phase error: 23.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→45.755 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -57.0304 Å / Origin y: -8.2123 Å / Origin z: -25.178 Å
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Refinement TLS group | Selection details: all |