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Yorodumi- PDB-5jeb: Crystal structure of EGFR tyrosine kinase domain with novel inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jeb | ||||||
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Title | Crystal structure of EGFR tyrosine kinase domain with novel inhibitor of active state of HER2 | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | Transferase/Transferase Inhibitor / Inhibitor / Kinase / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / tongue development / Inhibition of Signaling by Overexpressed EGFR ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / tongue development / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / midgut development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hydrogen peroxide metabolic process / ERBB2-EGFR signaling pathway / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / response to cobalamin / Signaling by ERBB4 / eyelid development in camera-type eye / protein insertion into membrane / 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 / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / cellular response to epidermal growth factor stimulus / EGFR Transactivation by Gastrin / transmembrane receptor protein tyrosine kinase activity / cellular response to cadmium ion / GRB2 events in ERBB2 signaling / positive regulation of DNA repair / neurogenesis / SHC1 events in ERBB2 signaling / regulation of ERK1 and ERK2 cascade / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / positive regulation of epithelial cell proliferation / neuron projection morphogenesis / epithelial cell proliferation / basal plasma membrane / positive regulation of superoxide anion generation / positive regulation of DNA replication / Signal transduction by L1 / cellular response to estradiol stimulus / liver regeneration / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / lung development / Signaling by ERBB2 TMD/JMD mutants / positive regulation of smooth muscle cell proliferation / EGFR downregulation / positive regulation of MAP kinase activity / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / negative regulation of protein catabolic process / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / kinase binding / peptidyl-tyrosine phosphorylation / Downregulation of ERBB2 signaling / cell-cell adhesion / positive regulation of miRNA transcription / ruffle membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.298 Å | ||||||
Authors | Park, J.H. / Lemmon, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Overcoming resistance to HER2 inhibitors through state-specific kinase binding. Authors: Novotny, C.J. / Pollari, S. / Park, J.H. / Lemmon, M.A. / Shen, W. / Shokat, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jeb.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jeb.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jeb_validation.pdf.gz | 757.7 KB | Display | wwPDB validaton report |
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Full document | 5jeb_full_validation.pdf.gz | 761.2 KB | Display | |
Data in XML | 5jeb_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 5jeb_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/5jeb ftp://data.pdbj.org/pub/pdb/validation_reports/je/5jeb | HTTPS FTP |
-Related structure data
Related structure data | 1m17S 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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Unit cell |
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-Components
#1: Protein | Mass: 38556.578 Da / Num. of mol.: 1 / Fragment: UNP residues 696-1022 / Mutation: V924R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P00533, receptor protein-tyrosine kinase | ||
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#2: Chemical | #3: Chemical | ChemComp-6JS / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 68.33 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.34M Ammonium sulfate, 1.34% (v/v) PEG 400, and 0.1M sodium acetate/acetic acid |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.298→50 Å / Num. obs: 8562 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rsym value: 0.057 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 3.298→3.36 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.26 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M17 Resolution: 3.298→34.717 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 368.44 Å2 / Biso mean: 149.818 Å2 / Biso min: 66.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.298→34.717 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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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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