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- PDB-2kv4: EGF -

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Basic information

Entry
Database: PDB / ID: 2kv4
TitleEGF
ComponentsEpidermal growth factor
KeywordsHORMONE / epithermal growth factor / EGF-like domain
Function / homology
Function and homology information


negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / 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 ...negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / positive regulation of epithelial tube formation / 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 / regulation of receptor signaling pathway via JAK-STAT / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / epidermal growth factor receptor binding / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / NFE2L2 regulating tumorigenic genes / positive regulation of DNA binding / PLCG1 events in ERBB2 signaling / positive regulation of peptidyl-threonine phosphorylation / ERBB2-EGFR signaling pathway / branching morphogenesis of an epithelial tube / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / ERBB2 Regulates Cell Motility / Signaling by ERBB4 / positive regulation of receptor internalization / PI3K events in ERBB2 signaling / mammary gland alveolus development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / GAB1 signalosome / positive regulation of phosphorylation / positive regulation of endothelial cell proliferation / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / positive regulation of endothelial cell migration / ERK1 and ERK2 cascade / 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 / Signaling by ERBB2 TMD/JMD mutants / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / 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 / Epidermal growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHuang, H.W. / Mohan, S.K. / Yu, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: The NMR solution structure of human epidermal growth factor (hEGF) at physiological pH and its interactions with suramin
Authors: Huang, H.W. / Mohan, S.K. / Yu, C.
History
DepositionMar 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Oct 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Epidermal growth factor


Theoretical massNumber of molelcules
Total (without water)6,2291
Polymers6,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Epidermal growth factor


Mass: 6229.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGF / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: Q6QBS2, UniProt: P01133*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein-1, 50 mM sodium phosphate-2, 20 mM sodium chloride-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
20 mMsodium chloride-31
Sample conditionsIonic strength: 0.07 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Michael Nilges, Institut Pasteurchemical shift assignment
ARIA1.1Michael Nilges, Institut Pasteurrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA/CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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