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- PDB-4b6u: Solution structure of eIF4E3 in complex with m7GDP -

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Basic information

Entry
Database: PDB / ID: 4b6u
TitleSolution structure of eIF4E3 in complex with m7GDP
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 3
KeywordsTRANSLATION
Function / homology
Function and homology information


ISG15 antiviral mechanism / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / translational initiation
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 4E type 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / XPLOR
AuthorsOsborne, M.J. / Volpon, L. / Kornblatt, J.A. / Culkjovic-Kraljcic, B. / Baguet, A. / Borden, K.L.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Eif4E3 Acts as a Tumor Suppressor by Utilizing an Atypical Mode of Methyl-7-Guanosine CAP Recognition
Authors: Osborne, M.J. / Volpon, L. / Kornblatt, J.A. / Culjkovic-Kraljcic, B. / Baguet, A. / Borden, K.L.B.
History
DepositionAug 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2May 4, 2016Group: Atomic model / Other
Revision 1.3Jan 17, 2018Group: Structure summary / Category: audit_author
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jun 19, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3222
Polymers22,8641
Non-polymers4581
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 3 / EIF-4E TYPE 3 / EIF-4E3 / EIF4E TYPE 3 / EIF4E-3


Mass: 22864.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9DBB5
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aliphatic
1213D 1H-15N NOESY
1313D 1H-13C NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 50MM PHOSPHATE, 100MM NACL, 100UM TCEP, NAN3, 90% WATER 10% D2
Sample conditionsIonic strength: 100 mM / pH: 7.2 / Pressure: 1 atm / Temperature: 300.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHBRUNGER SCHWIETERrefinement
NMRPipestructure solution
NMRViewstructure solution
RefinementMethod: XPLOR / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 10

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