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- PDB-2ogh: Solution structure of yeast eIF1 -

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Basic information

Entry
Database: PDB / ID: 2ogh
TitleSolution structure of yeast eIF1
ComponentsEukaryotic translation initiation factor eIF-1
KeywordsTRANSLATION / alpha-beta protein
Function / homology
Function and homology information


multi-eIF complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / ribosomal small subunit binding / regulation of translational fidelity / translation initiation factor binding / translation initiation factor activity / maintenance of translational fidelity / RNA binding
Similarity search - Function
SUI1-like domain / Translation Initiation Factor Eif1 / Eukaryotic translation initiation factor SUI1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor eIF-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsReibarkh, M. / del Rio, F. / Yamamoto, Y. / Asano, K. / Wagner, G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Eukaryotic Initiation Factor (eIF) 1 Carries Two Distinct eIF5-binding Faces Important for Multifactor Assembly and AUG Selection.
Authors: Reibarkh, M. / Yamamoto, Y. / Singh, C.R. / Del Rio, F. / Fahmy, A. / Lee, B. / Luna, R.E. / Ii, M. / Wagner, G. / Asano, K.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3Dec 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: Eukaryotic translation initiation factor eIF-1


Theoretical massNumber of molelcules
Total (without water)12,3301
Polymers12,3301
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 / 400target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Eukaryotic translation initiation factor eIF-1 / Protein translation factor SUI1


Mass: 12330.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUI1, RFR1 / Plasmid: pET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32911

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N,13C HNCO/HN(CA)CO
1313D 15N,13C HNCA/HN(CO)CA
1413D 15N,13C HN(CA)CB/HN(CO)CACB

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Sample preparation

DetailsContents: 50mM sodium phosphate, 300mM NaCl, 5mM bME, pH 7.2, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 300mM NaCl / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: CYANA / Developer: Guntert, P. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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