+Open data
-Basic information
Entry | Database: PDB / ID: 1jl9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Epidermal Growth Factor | ||||||
Components | EPIDERMAL GROWTH FACTOR | ||||||
Keywords | SIGNALING PROTEIN / Dimerization / Growth factor | ||||||
Function / homology | Function and homology information Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / negative regulation of secretion / negative regulation of cholesterol efflux / positive regulation of hyaluronan biosynthetic process / PLCG1 events in ERBB2 signaling / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / ERBB2-EGFR signaling pathway / positive regulation of epithelial tube formation ...Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / negative regulation of secretion / negative regulation of cholesterol efflux / positive regulation of hyaluronan biosynthetic process / PLCG1 events in ERBB2 signaling / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / ERBB2-EGFR signaling pathway / positive regulation of epithelial tube formation / ERBB2 Activates PTK6 Signaling / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / positive regulation of ubiquitin-dependent protein catabolic process / ERBB2 Regulates Cell Motility / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / PI3K events in ERBB2 signaling / regulation of receptor signaling pathway via JAK-STAT / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NFE2L2 regulating tumorigenic genes / epidermal growth factor receptor binding / branching morphogenesis of an epithelial tube / positive regulation of DNA binding / GAB1 signalosome / positive regulation of phosphorylation / positive regulation of receptor internalization / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / mammary gland alveolus development / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / epithelial cell proliferation / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of endothelial cell migration / positive regulation of mitotic nuclear division / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / platelet alpha granule lumen / guanyl-nucleotide exchange factor activity / positive regulation of peptidyl-threonine phosphorylation / Constitutive Signaling by EGFRvIII / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of cell migration / lysosomal membrane / positive regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 3 Å | ||||||
Authors | Lu, H.S. / Chai, J.J. / Li, M. / Huang, B.R. / He, C.H. / Bi, R.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of human epidermal growth factor and its dimerization Authors: Lu, H.S. / Chai, J.J. / Li, M. / Huang, B.R. / He, C.H. / Bi, R.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jl9.cif.gz | 22.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jl9.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jl9_validation.pdf.gz | 430.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jl9_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 1jl9_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1jl9_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/1jl9 ftp://data.pdbj.org/pub/pdb/validation_reports/jl/1jl9 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 5958.676 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01133 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.08 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: magnesium chloride, Bicine, CYMAL-3, sodium azide, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ROTATING ANODE / Site: APS / Type: RIGAKU RU200 |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. all: 21097 / Num. obs: 4040 / % possible obs: 99 % / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 100 Å / % possible obs: 99 % / Num. measured all: 21097 |
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 3→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber /
| ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
| ||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.231 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |