Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 89.46 kDa 
• Atom Count: 6005 
• Residue Count: 716 
• Unique protein chains: 1

2VGN

Structure of yeast Dom34 : a protein related to translation termination factor eRF1 and involved in No-Go decay.

• DOI: 10.2210/pdb2VGN/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-11-14 Released: 2008-01-22 
• Deposition Author(s): Graille, M., Chaillet, M., Van Tilbeurgh, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

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

• PubMed: 18180287 
• DOI: 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.

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Organizational Affiliation: 

Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, UMR8619-CNRS, IFR115, F-91405 Orsay, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DOM34	A, B	386	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DOM34, YNL001W, N2016 EC: 3.1
Find proteins for P33309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33309  Go to UniProtKB:  P33309

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 75.64	α = 90
b = 75.64	β = 90
c = 324.51	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-14 
• Released Date: 2008-01-22 
Deposition Author(s): Graille, M., Chaillet, M., Van Tilbeurgh, H.

Revision History 

• 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