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- PDB-1gk5: Solution Structure the mEGF/TGFalpha44-50 chimeric growth factor -

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Basic information

Entry
Database: PDB / ID: 1gk5
TitleSolution Structure the mEGF/TGFalpha44-50 chimeric growth factor
ComponentsPro-epidermal growth factor,Protransforming growth factor alpha
KeywordsGROWTH FACTOR / EGF GROWTH FACTOR / CHIMERIC
Function / homology
Function and homology information


Signaling by ERBB4 / EGFR interacts with phospholipase C-gamma / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / PI3K events in ERBB2 signaling / SHC1 events in ERBB2 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by ERBB2 / GAB1 signalosome ...Signaling by ERBB4 / EGFR interacts with phospholipase C-gamma / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / PI3K events in ERBB2 signaling / SHC1 events in ERBB2 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by ERBB2 / GAB1 signalosome / ERBB2 Regulates Cell Motility / NOTCH3 Activation and Transmission of Signal to the Nucleus / Downregulation of ERBB2 signaling / EGFR downregulation / negative regulation of secretion / regulation of protein transport / positive regulation of hyaluronan biosynthetic process / negative regulation of cholesterol efflux / hepatocyte proliferation / Extra-nuclear estrogen signaling / RAF/MAP kinase cascade / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / PIP3 activates AKT signaling / positive regulation of epithelial tube formation / Wnt receptor activity / Platelet degranulation / regulation of calcium ion import / positive regulation of protein localization to early endosome / Cargo recognition for clathrin-mediated endocytosis / regulation of protein localization to cell surface / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Wnt-protein binding / Clathrin-mediated endocytosis / positive regulation of ubiquitin-dependent protein catabolic process / Cargo concentration in the ER / regulation of receptor signaling pathway via JAK-STAT / COPII-mediated vesicle transport / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / positive regulation of DNA biosynthetic process / branching morphogenesis of an epithelial tube / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of receptor internalization / positive regulation of cell division / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / canonical Wnt signaling pathway / positive regulation of DNA binding / GAB1 signalosome / regulation of peptidyl-tyrosine phosphorylation / positive regulation of endothelial cell proliferation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / ERK1 and ERK2 cascade / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell migration / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / guanyl-nucleotide exchange factor activity / positive regulation of peptidyl-threonine phosphorylation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / EGFR downregulation / growth factor activity / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / epidermal growth factor receptor signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / 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 / cell population proliferation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome
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 / Coagulation Factor Xa inhibitory site ...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 / Coagulation Factor Xa inhibitory site / Laminin / 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 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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsChamberlin, S.G. / Brennan, L. / Puddicombe, S.M. / Davies, D.E. / Turner, D.L.
Citation
Journal: Eur.J.Biochem. / Year: 2001
Title: Solution Structure of the Megf/Tgfalpha44-50 Chimeric Growth Factor.
Authors: Chamberlin, S. / Brennan, L. / Puddicombe, S. / Davies, D. / Turner, D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The Interaction of an Epidermal Growth Factor/ Transforming Growth Factor Alpha Tail Chimera with the Human Epidermal Growth Factor Receptor Reveals Unexpected Complexities
Authors: Puddicombe, S.M. / Wood, L. / Chamberlin, S.G. / Davies, D.E.
History
DepositionAug 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pro-epidermal growth factor,Protransforming growth factor alpha


Theoretical massNumber of molelcules
Total (without water)5,2581
Polymers5,2581
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 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein/peptide Pro-epidermal growth factor,Protransforming growth factor alpha / EGF


Mass: 5257.785 Da / Num. of mol.: 1 / Fragment: UNP residues 977-1018,UNP residues 83-89
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89,THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES ...Details: THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89,THE PROTEIN IS A CHIMERA OF EPIDERMAL GROWTH FACTOR RESIDUES 977-1018 AND HUMAN TRANSFORMING GROWTH FACTOR ALPHA RESIDUES 83-89
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Egf, TGFA / Production host: Komagataella pastoris (fungus) / References: UniProt: P01132, UniProt: P01135

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D-1H-NOESY 2D-1H-TOCSY 2D-1H-COSY

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Sample preparation

Sample conditionspH: 3.0 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VXR500 / Manufacturer: Varian / Model: VXR500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
INDYANABRENNAN L, TURNER DL, MESSIAS AM, TEODORO ML, LEGALL J, SANTOS H, XAVIER AX.refinement
INDYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 10

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