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Yorodumi- PDB-2eb3: Crystal structure of mutated EGFR kinase domain (L858R) in comple... -
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-Basic information
Entry | Database: PDB / ID: 2eb3 | ||||||
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Title | Crystal structure of mutated EGFR kinase domain (L858R) in complex with AMPPNP | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE / Kinase / Tyrosine-protein kinase / Receptor / Phosphorylation / ATP-binding / Disease mutation / Transmembrane / Cell cycle / EC 2.7.10.1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 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 ...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 / 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / 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 / 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 / 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 / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of DNA repair / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / neurogenesis / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / cell-cell adhesion / ruffle membrane / positive regulation of miRNA transcription Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Yoshikawa, S. / Kukimoto-Niino, M. / Shirouzu, M. / Senba, K. / Yamamoto, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Oncogene / Year: 2012 Title: Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor Authors: Yoshikawa, S. / Kukimoto-Niino, M. / Parker, L. / Handa, N. / Terada, T. / Fujimoto, T. / Terazawa, Y. / Wakiyama, M. / Sato, M. / Sano, S. / Kobayashi, T. / Tanaka, T. / Chen, L. / Liu, Z.J. ...Authors: Yoshikawa, S. / Kukimoto-Niino, M. / Parker, L. / Handa, N. / Terada, T. / Fujimoto, T. / Terazawa, Y. / Wakiyama, M. / Sato, M. / Sano, S. / Kobayashi, T. / Tanaka, T. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Kawa, S. / Semba, K. / Yamamoto, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eb3.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eb3.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 2eb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2eb3 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2eb3 | HTTPS FTP |
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-Related structure data
Related structure data | 2eb2C 3ug1C 3ug2C 3vjnC 3vjoC 2gs2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38021.965 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 695-1022 / Mutation: L858R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: P00533, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-ANP / |
#3: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE IS SOMATIC MUTATION IN LUNG CANCER. |
-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: 62.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 0.1M Tris-HCl, 28% PEG 3000, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006 |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 12050 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 29.422 % / Biso Wilson estimate: 75.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 53.8 |
Reflection shell | Resolution: 2.84→2.94 Å / Redundancy: 29.9 % / Mean I/σ(I) obs: 5.833 / Rsym value: 0.814 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GS2 Resolution: 2.84→36.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 58204.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7616 Å2 / ksol: 0.338048 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.84→36.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→3.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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