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- PDB-2krb: Solution structure of EIF3B-RRM bound to EIF3J peptide -

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Basic information

Entry
Database: PDB / ID: 2krb
TitleSolution structure of EIF3B-RRM bound to EIF3J peptide
Components
  • Eukaryotic translation initiation factor 3 subunit B
  • Eukaryotic translation initiation factor 3 subunit J
KeywordsTRANSLATION / eIF3 / Translation initiation / eukaryotic initiation factor / eIF3b / eIF3j
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / molecular adaptor activity / synapse / RNA binding / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3-like domain superfamily / Translation initiation factor eIF3 subunit / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3-like domain superfamily / Translation initiation factor eIF3 subunit / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit J / Eukaryotic translation initiation factor 3 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsElantak, L. / Wagner, S. / Herrmannova, A. / Janoskova, M. / Rutkai, E. / Lukavsky, P.J. / Valasek, L.
CitationJournal: To be Published
Title: The indispensable N-terminal half of eIF3j/HCR1 co-operates with its structurally conserved binding partner eIF3b/PRT1-RRM and eIF1A in stringent AUG selection
Authors: Elantak, L. / Wagner, S. / Herrmannova, A. / Janoskova, M. / Rutkai, E. / Lukavsky, P.J. / Valasek, L.
History
DepositionDec 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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 3 subunit B
B: Eukaryotic translation initiation factor 3 subunit J


Theoretical massNumber of molelcules
Total (without water)10,5622
Polymers10,5622
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)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / eIF-3-eta / eIF3 p116 / eIF3 p110 / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / eIF-3-eta / eIF3 p116 / eIF3 p110 / Prt1 homolog / hPrt1


Mass: 9195.384 Da / Num. of mol.: 1 / Fragment: RRM domain, UNP residues 184-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: EIF3B, EIF3S9 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P55884
#2: Protein/peptide Eukaryotic translation initiation factor 3 subunit J / eIF3j / Eukaryotic translation initiation factor 3 subunit 1 / eIF-3-alpha / eIF3 p35


Mass: 1366.279 Da / Num. of mol.: 1 / Fragment: UNP residues 45-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: EIF3J, EIF3S1, PRO0391 / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: O75822

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
131NOESY
1432D filtered/edited NOESY
1523D 1H-15N NOESY
1623D 1H-13C NOESY
172NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] eIF3b-RRM, 0.85 mM eIF3j peptide, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM eIF3b-RRM, 0.85 mM [U-100% 13C; U-100% 15N] eIF3j peptide, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-100% 13C; U-100% 15N] eIF3b-RRM, 0.85 mM eIF3j peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMeIF3b-RRM[U-100% 13C; U-100% 15N]1
0.85 mMeIF3j peptide1
0.7 mMeIF3b-RRM2
0.85 mMeIF3j peptide[U-100% 13C; U-100% 15N]2
0.7 mMeIF3b-RRM[U-100% 13C; U-100% 15N]3
0.85 mMeIF3j peptide3
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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