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- PDB-4zjv: crystal structure of EGFR kinase domain in complex with Mitogen-i... -
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Basic information
Entry | Database: PDB / ID: 4zjv | ||||||
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Title | crystal structure of EGFR kinase domain in complex with Mitogen-inducible gene 6 protein | ||||||
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![]() | TRANSFERASE/INHIBITOR / Epidermal growth factor receptor (EGFR) / ERBB receptor feedback inhibitor 1 / Mitogen-inducible gene 6 protein(Mig6) / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / chondrocyte proliferation / regulation of keratinocyte differentiation / negative regulation of protein autophosphorylation / lung vasculature development / skin morphogenesis ...response to 1-oleoyl-sn-glycerol 3-phosphate / uterine epithelium development / limb joint morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / lung epithelium development / chondrocyte proliferation / regulation of keratinocyte differentiation / negative regulation of protein autophosphorylation / lung vasculature development / skin morphogenesis / tissue homeostasis / bile acid biosynthetic process / 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 / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / lung alveolus development / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / progesterone receptor signaling pathway / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / cellular response to cadmium ion / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / embryo implantation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / cholesterol metabolic process / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / liver development / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / protein localization to plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eck, M.J. / Park, E. / Lee, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.1 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.6 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r3pC ![]() 4r3rC ![]() 2rf9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37636.441 Da / Num. of mol.: 2 / Fragment: Kinase domain (UNP residues 695-1022) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, receptor protein-tyrosine kinase #2: Protein | Mass: 7803.705 Da / Num. of mol.: 2 / Fragment: UNP residues 330-399 / Mutation: S390C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris 0.2 M Ammonium acetate 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 23122 / % possible obs: 96.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RF9 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.084 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.178 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→50 Å
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