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- PDB-1k36: NMR Structure of human Epiregulin -

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Basic information

Entry
Database: PDB / ID: 1k36
TitleNMR Structure of human Epiregulin
ComponentsEpiregulin
KeywordsHORMONE/GROWTH FACTOR / EGF-like fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response ...luteinizing hormone signaling pathway / ovarian cumulus expansion / ovulation / ERBB4-ERBB4 signaling pathway / negative regulation of smooth muscle cell differentiation / ERBB2-ERBB4 signaling pathway / primary follicle stage / female meiotic nuclear division / PI3K events in ERBB4 signaling / positive regulation of innate immune response / mRNA transcription / oocyte maturation / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / ERBB2 Regulates Cell Motility / positive regulation of cell division / PI3K events in ERBB2 signaling / keratinocyte proliferation / SHC1 events in ERBB4 signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / anatomical structure morphogenesis / positive regulation of protein kinase activity / GAB1 signalosome / Nuclear signaling by ERBB4 / positive regulation of phosphorylation / keratinocyte differentiation / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / positive regulation of mitotic nuclear division / positive regulation of DNA replication / positive regulation of cytokine production / EGFR downregulation / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / clathrin-coated endocytic vesicle membrane / wound healing / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / response to peptide hormone / Downregulation of ERBB2 signaling / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Constitutive Signaling by Aberrant PI3K in Cancer / negative regulation of epithelial cell proliferation / positive regulation of fibroblast proliferation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / cell-cell signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / receptor ligand activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Laminin / Laminin / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsSato, K. / Miura, K. / Tada, M. / Aizawa, T. / Miyamoto, K. / Kawano, K.
CitationJournal: Febs Lett. / Year: 2003
Title: Solution structure of epiregulin and the effect of its C-terminal domain for receptor binding affinity
Authors: Sato, K. / Nakamura, T. / Mizuguchi, M. / Miura, K. / Tada, M. / Aizawa, T. / Gomi, T. / Miyamoto, K. / Kawano, K.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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: Epiregulin


Theoretical massNumber of molelcules
Total (without water)5,2801
Polymers5,2801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide Epiregulin /


Mass: 5280.072 Da / Num. of mol.: 1 / Fragment: residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: O14944

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
2422D NOESY
252DQF-COSY
2622D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Epiregulin, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM Epiregulin, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 3.4 1 atm303 K
20 3.4 1 atm303 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 604 restraints, 556 are NOE-derived distance constraints, 38 dihedral angle restraints, 10 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 40

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