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- PDB-1ip0: NMR STRUCTURE OF HUMAN BETACELLULIN-2 -

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Basic information

Entry
Database: PDB / ID: 1ip0
TitleNMR STRUCTURE OF HUMAN BETACELLULIN-2
ComponentsBETACELLULIN
KeywordsHORMONE/GROWTH FACTOR / EGF-like fold / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


ERBB4-ERBB4 signaling pathway / positive regulation of urine volume / PI3K events in ERBB4 signaling / negative regulation of epithelial cell apoptotic process / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epithelial cell apoptotic process / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / ERBB2 Activates PTK6 Signaling ...ERBB4-ERBB4 signaling pathway / positive regulation of urine volume / PI3K events in ERBB4 signaling / negative regulation of epithelial cell apoptotic process / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epithelial cell apoptotic process / 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 / SHC1 events in ERBB4 signaling / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / GAB1 signalosome / Nuclear signaling by ERBB4 / 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 cell differentiation / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / growth factor activity / clathrin-coated endocytic vesicle membrane / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Downregulation of ERBB2 signaling / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / cell population proliferation / Extra-nuclear estrogen signaling / receptor ligand activity / 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
AuthorsMiura, K. / Doura, H. / Aizawa, T. / Tada, H. / Seno, M. / Yamada, H. / Kawano, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Solution structure of betacellulin, a new member of EGF-family ligands.
Authors: Miura, K. / Doura, H. / Aizawa, T. / Tada, H. / Seno, M. / Yamada, H. / Kawano, K.
History
DepositionApr 19, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2002Provider: 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETACELLULIN


Theoretical massNumber of molelcules
Total (without water)5,9171
Polymers5,9171
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)1 / 50structures with the lowest energy
Representative

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Components

#1: Protein/peptide BETACELLULIN


Mass: 5916.886 Da / Num. of mol.: 1 / Fragment: RESIDUES 62-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBO41 / Production host: Escherichia coli (E. coli) / References: UniProt: P35070

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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
12.0mM Betacellulin-2, 1.0% acetate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
22.0mM Betacellulin-2, 1.0% acetate buffer, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.28 3.5 1 atm298 K
20.28 3.5 1 atm298 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 538 restraints, 461 are NOE-derived distance constraints, 41 dihedral angle restraints,36 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 1

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