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- PDB-1a3p: ROLE OF THE 6-20 DISULFIDE BRIDGE IN THE STRUCTURE AND ACTIVITY O... -

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Basic information

Entry
Database: PDB / ID: 1a3p
TitleROLE OF THE 6-20 DISULFIDE BRIDGE IN THE STRUCTURE AND ACTIVITY OF EPIDERMAL GROWTH FACTOR, NMR, 20 STRUCTURES
ComponentsEPIDERMAL GROWTH FACTOR
KeywordsGROWTH FACTOR / MURINE EPIDERMAL GROWTH FACTOR / DISULFIDE CONNECTIVITIES / EGF-LIKE DOMAIN
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 / ERBB2 Regulates Cell Motility ...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 / ERBB2 Regulates Cell Motility / GAB1 signalosome / 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 / RAF/MAP kinase cascade / Extra-nuclear estrogen signaling / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / PIP3 activates AKT signaling / Platelet degranulation / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / Cargo recognition for clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Clathrin-mediated endocytosis / positive regulation of epithelial tube formation / positive regulation of ubiquitin-dependent protein catabolic process / regulation of receptor signaling pathway via JAK-STAT / ERBB2-EGFR signaling pathway / positive regulation of DNA biosynthetic process / epidermal growth factor receptor binding / branching morphogenesis of an epithelial tube / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of receptor internalization / mammary gland alveolus development / positive regulation of DNA binding / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / ERK1 and ERK2 cascade / positive regulation of endothelial cell proliferation / guanyl-nucleotide exchange factor activity / positive regulation of mitotic nuclear division / positive regulation of endothelial cell migration / positive regulation of peptidyl-threonine phosphorylation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / epidermal growth factor receptor signaling pathway / positive regulation of canonical Wnt signaling pathway / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / angiogenesis / cell population proliferation / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / calcium ion binding / positive regulation of cell population proliferation / 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 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBarnham, K. / Torres, A. / Alewood, D. / Alewood, P. / Domagala, T. / Nice, E. / Norton, R.
CitationJournal: Protein Sci. / Year: 1998
Title: Role of the 6-20 disulfide bridge in the structure and activity of epidermal growth factor.
Authors: Barnham, K.J. / Torres, A.M. / Alewood, D. / Alewood, P.F. / Domagala, T. / Nice, E.C. / Norton, R.S.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_exptl_sample_conditions ...pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _pdbx_nmr_exptl_sample_conditions.pressure_units / _struct_ref_seq_dif.details

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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)4,8781
Polymers4,8781
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100020 BEST, BASED ON STEREOCHEMICAL AND NOE ENERGIES
RepresentativeModel #1

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Components

#1: Protein/peptide EPIDERMAL GROWTH FACTOR / / [ABU6 / 20] MEGF4-48


Mass: 4878.402 Da / Num. of mol.: 1 / Fragment: RESIDUES 4 - 48
Mutation: DEL(1-3, 49-53), C6(AMINO-BUTYRIC ACID), C20 (AMINO-BUTYRIC ACID)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01132

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOSEY
121DQF-COSY
131TOCSY
141E-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 2D METHODS.

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Sample preparation

DetailsContents: H2O
Sample conditionspH: 2.8 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
DYANAstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: 20 BEST, BASED ON STEREOCHEMICAL AND NOE ENERGIES
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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