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- PDB-1p9j: Solution structure and dynamics of the EGF/TGF-alpha chimera T1E -

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Basic information

Entry
Database: PDB / ID: 1p9j
TitleSolution structure and dynamics of the EGF/TGF-alpha chimera T1E
Componentschimera of Epidermal growth factor(EGF) and Transforming growth factor alpha (TGF-alpha)
KeywordsHORMONE/GROWTH FACTOR / chimera / EGF / TGF-alpha / ErbB1 / ErbB3 / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / hepatocyte proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / positive regulation of epithelial tube formation ...negative regulation of secretion / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / hepatocyte proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / positive regulation of epithelial tube formation / positive regulation of ubiquitin-dependent protein catabolic process / Cargo concentration in the ER / regulation of receptor signaling pathway via JAK-STAT / Inhibition of Signaling by Overexpressed EGFR / COPII-mediated vesicle transport / EGFR interacts with phospholipase C-gamma / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / NFE2L2 regulating tumorigenic genes / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / branching morphogenesis of an epithelial tube / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / positive regulation of receptor internalization / positive regulation of cell division / PI3K events in ERBB2 signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / positive regulation of DNA binding / GAB1 signalosome / positive regulation of phosphorylation / Signaling by ERBB2 / ERK1 and ERK2 cascade / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in ERBB2 signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell proliferation / SHC1 events in ERBB2 signaling / guanyl-nucleotide exchange factor activity / positive regulation of mitotic nuclear division / positive regulation of endothelial cell migration / platelet alpha granule lumen / positive regulation of peptidyl-threonine phosphorylation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / ER to Golgi transport vesicle membrane / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / positive regulation of canonical Wnt signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / PIP3 activates AKT signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / intracellular signal transduction / lysosomal membrane / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / 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 / Coagulation Factor Xa inhibitory site / Laminin / 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 / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Pro-epidermal growth factor / Protransforming growth factor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, brief molecular dynamics run in water.
AuthorsWingens, M. / Walma, T. / Van Ingen, H. / Stortelers, C. / Van Leeuwen, J.E. / Van Zoelen, E.J. / Vuister, G.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Analysis of an Epidermal Growth Factor/Transforming Growth Factor-alpha Chimera with Unique ErbB Binding Specificity.
Authors: Wingens, M. / Walma, T. / Van Ingen, H. / Stortelers, C. / Van Leeuwen, J.E. / Van Zoelen, E.J. / Vuister, G.W.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimera of Epidermal growth factor(EGF) and Transforming growth factor alpha (TGF-alpha)


Theoretical massNumber of molelcules
Total (without water)6,3391
Polymers6,3391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)36 / 98structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein chimera of Epidermal growth factor(EGF) and Transforming growth factor alpha (TGF-alpha)


Mass: 6339.224 Da / Num. of mol.: 1 / Fragment: TGF-alpha (residues 1-7), EGF (residues 8-54)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGF-alpha and EGF / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P01135, UniProt: P01133

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.8mM T1E, 15N-labelled, 50mM phosphate buffer, 95% H20, 5%D20, pH 6.3, 20ug/mL pefabloc
Solvent system: 95% H20, 5%D20, pH 6.3
Sample conditionsIonic strength: 50 / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe203Delaglio, F.processing
X-PLOR3.851Brunger, A.refinement
CHARMM22MacKerell, A.D.refinement
RefinementMethod: distance geometry, brief molecular dynamics run in water.
Software ordinal: 1
Details: The structures are based on 660 are NOE-derived distance constraints, 98 dihedral angle restraints, and 9 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 98 / Conformers submitted total number: 36

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