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- PDB-2mx4: NMR structure of Phosphorylated 4E-BP2 -

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Basic information

Entry
Database: PDB / ID: 2mx4
TitleNMR structure of Phosphorylated 4E-BP2
ComponentsEukaryotic translation initiation factor 4E-binding protein 2
KeywordsTranslation / protein Binding / phosphorylation / intrinsic disorder
Function / homology
Function and homology information


neuronal ribonucleoprotein granule / eukaryotic initiation factor 4E binding / intracellular membraneless organelle / social behavior / TOR signaling / translation repressor activity / negative regulation of translational initiation / modulation of chemical synaptic transmission / regulation of synaptic plasticity / memory ...neuronal ribonucleoprotein granule / eukaryotic initiation factor 4E binding / intracellular membraneless organelle / social behavior / TOR signaling / translation repressor activity / negative regulation of translational initiation / modulation of chemical synaptic transmission / regulation of synaptic plasticity / memory / insulin receptor signaling pathway / postsynapse / translation / nucleus / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding / Eukaryotic translation initiation factor 4E binding protein (EIF4EBP)
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBah, A. / Forman-Kay, J. / Vernon, R. / Siddiqui, Z. / Krzeminski, M. / Muhandiram, R. / Zhao, C. / Sonenberg, N. / Kay, L.
CitationJournal: Nature / Year: 2015
Title: Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch.
Authors: Bah, A. / Vernon, R.M. / Siddiqui, Z. / Krzeminski, M. / Muhandiram, R. / Zhao, C. / Sonenberg, N. / Kay, L.E. / Forman-Kay, J.D.
History
DepositionDec 10, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E-binding protein 2


Theoretical massNumber of molelcules
Total (without water)5,0911
Polymers5,0911
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 / 20359structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Eukaryotic translation initiation factor 4E-binding protein 2 / 4E-BP2 / eIF4E-binding protein 2


Mass: 5090.515 Da / Num. of mol.: 1 / Fragment: residues 18-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4EBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13542
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D H(CCO)NH
1413D 1H-15N NOESY
1513D CBCA(CO)NH
1613D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] Phosphorylated 4E-BP2, 2 mM DTT, 100 mM sodium chloride, 30 mM sodium phosphate, 1 mM EDTA, 1 mM Benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPhosphorylated 4E-BP2-1[U-99% 13C; U-99% 15N]1
2 mMDTT-21
100 mMsodium chloride-31
30 mMsodium phosphate-41
1 mMEDTA-51
1 mMBenzamidine-61
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 20 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipeGoddardprocessing
NMRPipeGoddardchemical shift assignment
NMRPipeGoddardstructure solution
NMRPipeShen, Vernon, Baker and Baxprocessing
NMRPipeShen, Vernon, Baker and Baxchemical shift assignment
NMRPipeShen, Vernon, Baker and Baxstructure solution
CS-ROSETTALange and Bakerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20359 / Conformers submitted total number: 20

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