4K51

Crystal Structure of the PCI domain of eIF3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes.

Khoshnevis, S.Gunisova, S.Vlckova, V.Kouba, T.Neumann, P.Beznoskova, P.Ficner, R.Valasek, L.S.

(2014) Nucleic Acids Res 42: 4123-4139

  • DOI: https://doi.org/10.1093/nar/gkt1369
  • Primary Citation of Related Structures:  
    4K51

  • PubMed Abstract: 

    Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 43-48S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65-Å resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs.


  • Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Microbiology and Genetics, George-August University, Goettingen, Germany, 37077 and Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, Videnska 1083, 142 20 Prague, the Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit A
A, B
224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPG1TIF32YBR079CYBR0734
UniProt
Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38249 
Go to UniProtKB:  P38249
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38249
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.14α = 90
b = 137.14β = 90
c = 137.14γ = 90
Software Package:
Software NamePurpose
SHARPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references