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Yorodumi- PDB-3ltg: Crystal structure of the Drosophila Epidermal Growth Factor Recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ltg | ||||||
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Title | Crystal structure of the Drosophila Epidermal Growth Factor Receptor ectodomain complexed with a low affinity Spitz mutant | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE REGULATOR / Receptor-Ligand complex ectodomain cysteine rich domain EGF domain / ATP-binding / Kinase / Nucleotide-binding / Receptor / Transferase / Tyrosine-protein kinase / Cell membrane / Developmental protein / Differentiation / Disulfide bond / EGF-like domain / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Membrane / Neurogenesis / Transmembrane / TRANSFERASE-TRANSFERASE REGULATOR complex | ||||||
Function / homology | Function and homology information notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling ...notum development / leg disc proximal/distal pattern formation / maternal determination of dorsal/ventral axis, ovarian follicular epithelium, soma encoded / regulation of tube length, open tracheal system / wing and notum subfield formation / notum cell fate specification / R8 cell differentiation / Signaling by ERBB2 / Signaling by ERBB4 / SHC1 events in ERBB2 signaling / PI3K events in ERBB4 signaling / Nuclear signaling by ERBB4 / Signaling by EGFR / PI3K events in ERBB2 signaling / EGFR interacts with phospholipase C-gamma / ERBB2 Regulates Cell Motility / Drug-mediated inhibition of ERBB2 signaling / ectodermal cell fate determination / oenocyte differentiation / dorsal closure, spreading of leading edge cells / stomatogastric nervous system development / maintenance of epithelial integrity, open tracheal system / lumen formation, open tracheal system / positive regulation of imaginal disc growth / stem cell fate commitment / photoreceptor cell fate determination / salivary gland development / imaginal disc development / photoreceptor cell differentiation / morphogenesis of follicular epithelium / epithelial cell proliferation involved in Malpighian tubule morphogenesis / PIP3 activates AKT signaling / GAB1 signalosome / Sema4D induced cell migration and growth-cone collapse / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / compound eye cone cell differentiation / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / Malpighian tubule morphogenesis / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / determination of genital disc primordium / Downregulation of ERBB2:ERBB3 signaling / Downregulation of ERBB2 signaling / tracheal outgrowth, open tracheal system / haltere development / compound eye photoreceptor cell differentiation / germ-band shortening / ommatidial rotation / negative regulation of compound eye retinal cell programmed cell death / Downregulation of ERBB4 signaling / oenocyte development / EGFR downregulation / imaginal disc-derived wing vein morphogenesis / chorion-containing eggshell pattern formation / Cargo recognition for clathrin-mediated endocytosis / dorsal closure / establishment or maintenance of apical/basal cell polarity / spiracle morphogenesis, open tracheal system / wing disc morphogenesis / imaginal disc-derived wing vein specification / Clathrin-mediated endocytosis / dorsal appendage formation / border follicle cell migration / Estrogen-dependent gene expression / compound eye development / positive regulation of border follicle cell migration / segment polarity determination / imaginal disc-derived wing morphogenesis / oocyte axis specification / gonad development / germ-line stem cell population maintenance / eye development / behavioral response to ethanol / heart process / olfactory learning / embryonic pattern specification / peripheral nervous system development / establishment of epithelial cell apical/basal polarity / cell projection assembly / embryo development ending in birth or egg hatching / epidermal growth factor receptor activity / positive regulation of neurogenesis / digestive tract morphogenesis / epidermal growth factor receptor binding / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of wound healing / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of apoptotic signaling pathway / positive regulation of cell division / positive regulation of phosphorylation / transmembrane receptor protein tyrosine kinase activity / neurogenesis / basal plasma membrane / determination of adult lifespan / morphogenesis of an epithelium Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Alvarado, D. / Klein, D.E. / Lemmon, M.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2010 Title: Structural basis for negative cooperativity in growth factor binding to an EGF receptor. Authors: Alvarado, D. / Klein, D.E. / Lemmon, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ltg.cif.gz | 222.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ltg.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ltg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/3ltg ftp://data.pdbj.org/pub/pdb/validation_reports/lt/3ltg | HTTPS FTP |
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-Related structure data
Related structure data | 3ltfSC 3i2tS S: Starting model for refinement C: citing same article (ref.) |
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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: 67970.914 Da / Num. of mol.: 2 / Fragment: ectodomain, residues 100-688 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: torpedo; dEGFR / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P04412, Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases #2: Protein | | Mass: 6012.862 Da / Num. of mol.: 1 / Fragment: EGF domain, residues 76-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Spitz / Plasmid: pMT / Cell line (production host): Schneider 2(S2) cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01083 |
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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: 4.29 Å3/Da / Density % sol: 71.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 11% PEG 20,000 0.1M HEPES pH7.4 3% n-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97928 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2007 |
Radiation | Monochromator: double crystal monochromator and K-B pair of biomorph mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 28593 / Num. obs: 28590 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rsym value: 0.083 / Net I/σ(I): 17 |
Reflection shell | Resolution: 3.4→3.57 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.496 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I2T and 3LTF; s-dEGFR ectodomain unliganded and complexed with Spitz Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.77 / Cor.coef. Fo:Fc free: 0.748 / SU B: 0.006 / SU ML: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.876 / ESU R Free: 0.922 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.04 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
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LS refinement shell | Resolution: 3.4→3.485 Å / Total num. of bins used: 20
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