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- PDB-1ap8: TRANSLATION INITIATION FACTOR EIF4E IN COMPLEX WITH M7GDP, NMR, 2... -

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Basic information

Entry
Database: PDB / ID: 1ap8
TitleTRANSLATION INITIATION FACTOR EIF4E IN COMPLEX WITH M7GDP, NMR, 20 STRUCTURES
ComponentsTRANSLATION INITIATION FACTOR EIF4E
KeywordsRNA CAP / TRANSLATION INITIATION FACTOR
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / positive regulation of formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / phosphatidylinositol-3-phosphate binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor activity / translational initiation / cytoplasmic stress granule / regulation of cell cycle / ribosome / nucleus / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
AuthorsMatsuo, H. / Li, H. / Mcguire, A.M. / Fletcher, M. / Gingras, A.C. / Sonenberg, N. / Wagner, G.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structure of translation factor eIF4E bound to m7GDP and interaction with 4E-binding protein.
Authors: Matsuo, H. / Li, H. / McGuire, A.M. / Fletcher, C.M. / Gingras, A.C. / Sonenberg, N. / Wagner, G.
History
DepositionJul 25, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 6, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSLATION INITIATION FACTOR EIF4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7452
Polymers24,2871
Non-polymers4581
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 / 60NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE
Representative

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Components

#1: Protein TRANSLATION INITIATION FACTOR EIF4E


Mass: 24287.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: BL21 (DE3) / Plasmid: BL21 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P07260
#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
111NOESY (1H
12113C
13115N)
141HCCHTOCSY
151CT-HNCA
161CT-HN(CO)CA
171HN(CA)CB
181HN(CO)CACB
191HN(CA)CO-D
1101HNCO
1111HN(COCA)NH
1121HN(CA)HA
1131HN(COCA)HA
1141HCC (CO)NNH

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUS750VarianUNITYPLUS7507501
Varian UNITY500VarianUNITY5005002
Varian UNITYPLUS500VarianUNITYPLUS5005003

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE
Conformers calculated total number: 60 / Conformers submitted total number: 20

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