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- PDB-2rnl: Solution structure of the EGF-like domain from human Amphiregulin -

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Basic information

Entry
Database: PDB / ID: 2rnl
TitleSolution structure of the EGF-like domain from human Amphiregulin
ComponentsAmphiregulin
KeywordsSIGNALING PROTEIN / AR / Colorectum cell-derived growth factor / EGF-like domain / CRDGF / Cytokine / Glycoprotein / Membrane / Polymorphism / Transmembrane / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis / positive regulation of epidermal growth factor-activated receptor activity / positive regulation of keratinocyte proliferation / mammary gland branching involved in thelarche / clathrin-coated vesicle membrane / COPII vesicle coating / membrane organization / Cargo concentration in the ER / COPII-mediated vesicle transport / Inhibition of Signaling by Overexpressed EGFR ...dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis / positive regulation of epidermal growth factor-activated receptor activity / positive regulation of keratinocyte proliferation / mammary gland branching involved in thelarche / clathrin-coated vesicle membrane / COPII vesicle coating / membrane organization / Cargo concentration in the ER / COPII-mediated vesicle transport / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor binding / Signaling by EGFR / epithelial cell proliferation involved in mammary gland duct elongation / negative regulation of epidermal growth factor receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / negative regulation of osteoblast differentiation / GAB1 signalosome / glial cell proliferation / endoplasmic reticulum to Golgi vesicle-mediated transport / response to glucocorticoid / response to cAMP / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / cytokine activity / EGFR downregulation / growth factor activity / response to hydrogen peroxide / ER to Golgi transport vesicle membrane / epidermal growth factor receptor signaling pathway / response to peptide hormone / Constitutive Signaling by Aberrant PI3K in Cancer / neuron projection development / MAPK cascade / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / response to estradiol / cell-cell signaling / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / membrane => GO:0016020 / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / positive regulation of cell population proliferation / endoplasmic reticulum membrane / cell surface / signal transduction / extracellular space / extracellular region / nucleus
Similarity search - Function
Laminin / Laminin / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X. / Hayashi, F. / Terada, T. / Shirouzu, M. / Watanabe, S. / Kigawa, T. / Yabuta, N. / Nojima, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the EGF-like domain from human Amphiregulin
Authors: Qin, X. / Hayashi, F. / Terada, T. / Shirouzu, M. / Watanabe, S. / Kigawa, T. / Yabuta, N. / Nojima, H. / Yokoyama, S.
History
DepositionJan 11, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amphiregulin


Theoretical massNumber of molelcules
Total (without water)5,5841
Polymers5,5841
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Amphiregulin / AR / Colorectum cell-derived growth factor / CRDGF


Mass: 5584.219 Da / Num. of mol.: 1 / Fragment: EGF-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E. coli CELL-FREE / Gene: AREG, SDGF / Production host: CELL-FREE PROTEIN SYNTHESIS / References: UniProt: P15514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 20mM [U-100% 2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 10% [U-100% 2H] D2O; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRIS[U-100% 2H]1
100 mMsodium chloride1
0.02 %sodium azide1
10 %D2O[U-100% 2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20030801Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
KUJIRA0.982Kobayashi,N.data analysis
KUJIRA0.982Kobayashi,N.chemical shift assignment
KUJIRA0.982Kobayashi,N.peak picking
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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