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- PDB-2g2k: NMR structure of an N-terminal fragment of the eukaryotic initiat... -

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Basic information

Entry
Database: PDB / ID: 2g2k
TitleNMR structure of an N-terminal fragment of the eukaryotic initiation factor 5 (eIF5)
ComponentsEukaryotic translation initiation factor 5
KeywordsTRANSLATION / eIF5 / eIF125 fold
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / formation of cytoplasmic translation initiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor activity / GTPase activator activity / ribosome assembly / cadherin binding ...eukaryotic initiation factor eIF2 binding / formation of cytoplasmic translation initiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor activity / GTPase activator activity / ribosome assembly / cadherin binding / synapse / GTP binding / RNA binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #350 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain ...N-terminal domain of TfIIb - #350 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / N-terminal domain of TfIIb / Single Sheet / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsConte, M.R. / Kelly, G. / Babon, J. / Sanfelice, D. / Smerdon, S.J. / Proud, C.G.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of the eukaryotic initiation factor (eIF) 5 reveals a fold common to several translation factors
Authors: Conte, M.R. / Kelly, G. / Babon, J. / Sanfelice, D. / Youell, J. / Smerdon, S.J. / Proud, C.G.
History
DepositionFeb 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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 5


Theoretical massNumber of molelcules
Total (without water)19,2741
Polymers19,2741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic translation initiation factor 5 / eIF-5


Mass: 19274.211 Da / Num. of mol.: 1 / Fragment: N-terminal fragment, residues 1-170 / Mutation: S10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55010

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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 13C-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 0.6mM U-15N, 13C; 20mM sodium acetate / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: No added salt / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
NMRPipelatestDalaglioprocessing
X-PLOR3.1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 18

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