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- PDB-1jl9: Crystal Structure of Human Epidermal Growth Factor -

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Basic information

Entry
Database: PDB / ID: 1jl9
TitleCrystal Structure of Human Epidermal Growth Factor
ComponentsEPIDERMAL GROWTH FACTOR
KeywordsSIGNALING PROTEIN / Dimerization / Growth factor
Function / homology
Function and homology information


positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / negative regulation of secretion / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / cerebellar granule cell precursor proliferation / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / regulation of calcium ion import / transmembrane receptor protein tyrosine kinase activator activity ...positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / negative regulation of secretion / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / cerebellar granule cell precursor proliferation / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / regulation of calcium ion import / transmembrane receptor protein tyrosine kinase activator activity / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of ubiquitin-dependent protein catabolic process / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / epidermal growth factor receptor binding / positive regulation of peptidyl-threonine phosphorylation / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / regulation of receptor signaling pathway via JAK-STAT / positive regulation of DNA binding / NFE2L2 regulating tumorigenic genes / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / branching morphogenesis of an epithelial tube / Signaling by EGFR / ERBB2 Regulates Cell Motility / positive regulation of receptor internalization / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / mammary gland alveolus development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / GAB1 signalosome / Signaling by ERBB2 / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / positive regulation of endothelial cell migration / GRB2 events in ERBB2 signaling / positive regulation of mitotic nuclear division / SHC1 events in ERBB2 signaling / platelet alpha granule lumen / guanyl-nucleotide exchange factor activity / epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / growth factor activity / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of canonical Wnt signaling pathway / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / receptor ligand activity / 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
Pro-epidermal growth factor / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Laminin ...Pro-epidermal growth factor / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Pro-epidermal growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3 Å
AuthorsLu, H.S. / Chai, J.J. / Li, M. / Huang, B.R. / He, C.H. / Bi, R.C.
CitationJournal: 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
DepositionJul 16, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPIDERMAL GROWTH FACTOR
B: EPIDERMAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)11,9172
Polymers11,9172
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.43, 61.43, 87.04
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EPIDERMAL GROWTH FACTOR / EGF


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 / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.9 M1reservoirMgCl2
23.5 mMCYMAL-31reservoir
30.1 MBicine1reservoir
450 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Site: APS / Type: RIGAKU RU200
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→100 Å / Num. all: 21097 / Num. obs: 4040 / % possible obs: 99 % / Rmerge(I) obs: 0.104
Reflection shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 3→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber /
RfactorSelection details
Rfree0.283 RANDOM
Rwork0.231 -
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 0 0 7 704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.193
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

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