Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (SelenoMet-labeled protein)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Structure of Yeast Dom34: A Protein Related to Translation Termination Factor Erf1 and Involved in No-Go Decay.

Graille, M.Chaillet, M.Van Tilbeurgh, H.

(2008) J Biol Chem 283: 7145

  • DOI: https://doi.org/10.1074/jbc.M708224200
  • Primary Citation of Related Structures:  
    2VGM, 2VGN

  • PubMed Abstract: 

    The yeast protein Dom34 has been described to play a critical role in a newly identified mRNA decay pathway called No-Go decay. This pathway clears cells from mRNAs inducing translational stalls through endonucleolytic cleavage. Dom34 is related to the translation termination factor eRF1 and physically interacts with Hbs1, which is itself related to eRF3. We have solved the 2.5-A resolution crystal structure of Saccharomyces cerevisiae Dom34. This protein is organized in three domains with the central and C-terminal domains structurally homologous to those from eRF1. The N-terminal domain of Dom34 is different from eRF1. It adopts a Sm-fold that is often involved in the recognition of mRNA stem loops or in the recruitment of mRNA degradation machinery. The comparison of eRF1 and Dom34 domains proposed to interact directly with eRF3 and Hbs1, respectively, highlights striking structural similarities with eRF1 motifs identified to be crucial for the binding to eRF3. In addition, as observed for eRF1 that enhances eRF3 binding to GTP, the interaction of Dom34 with Hbs1 results in an increase in the affinity constant of Hbs1 for GTP but not GDP. Taken together, these results emphasize that eukaryotic cells have evolved two structurally related complexes able to interact with ribosomes either paused at a stop codon or stalled in translation by the presence of a stable stem loop and to trigger ribosome release by catalyzing chemical bond hydrolysis.

  • Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, UMR8619-CNRS, IFR115, F-91405 Orsay, France. marc.graille@u-psud.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DOM34YNL001WN2016
EC: 3.1
Find proteins for P33309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33309 
Go to UniProtKB:  P33309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33309
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.64α = 90
b = 75.64β = 90
c = 324.51γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.4: 2021-03-17
    Changes: Derived calculations, Other, Structure summary