4LUN

Structure of the N-terminal mIF4G domain from S. cerevisiae Upf2, a protein involved in the degradation of mRNAs containing premature stop codons


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A highly conserved region essential for NMD in the Upf2 N-terminal domain.

Fourati, Z.Roy, B.Millan, C.Coureux, P.D.Kervestin, S.van Tilbeurgh, H.He, F.Uson, I.Jacobson, A.Graille, M.

(2014) J Mol Biol 426: 3689-3702

  • DOI: 10.1016/j.jmb.2014.09.015
  • Primary Citation of Related Structures:  
    4LUN

  • PubMed Abstract: 
  • Upf1, Upf2, and Upf3 are the principal regulators of nonsense-mediated mRNA decay (NMD), a cytoplasmic surveillance pathway that accelerates the degradation of mRNAs undergoing premature translation termination. These three proteins interact with each other, the ribosome, the translation termination machinery, and multiple mRNA decay factors, but the precise mechanism allowing the selective detection and degradation of nonsense-containing transcripts remains elusive ...

    Upf1, Upf2, and Upf3 are the principal regulators of nonsense-mediated mRNA decay (NMD), a cytoplasmic surveillance pathway that accelerates the degradation of mRNAs undergoing premature translation termination. These three proteins interact with each other, the ribosome, the translation termination machinery, and multiple mRNA decay factors, but the precise mechanism allowing the selective detection and degradation of nonsense-containing transcripts remains elusive. Here, we have determined the crystal structure of the N-terminal mIF4G domain from Saccharomyces cerevisiae Upf2 and identified a highly conserved region in this domain that is essential for NMD and independent of Upf2's binding sites for Upf1 and Upf3. Mutations within this conserved region not only inactivate NMD but also disrupt Upf2 binding to specific proteins, including Dbp6, a DEAD-box helicase. Although current models indicate that Upf2 functions principally as an activator of Upf1 and a bridge between Upf1 and Upf3, our data suggest that it may also serve as a platform for the association of additional factors that play roles in premature translation termination and NMD.


    Organizational Affiliation

    Laboratoire de Biochimie, CNRS UMR 7654, Ecole Polytechnique, F-91128 Palaiseau Cedex, France; Institut de Biochimie et Biophysique Moléculaire et Cellulaire, CNRS UMR 8619, Université Paris Sud, F-91405 Orsay Cedex, France. Electronic address: marc.graille@polytechnique.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nonsense-mediated mRNA decay protein 2A [auth U]316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IFS1NMD2SUA1UPF2YHR077C
UniProt
Find proteins for P38798 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38798 
Go to UniProtKB:  P38798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38798
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth U]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.813α = 90
b = 50.927β = 99.96
c = 71.993γ = 90
Software Package:
Software NamePurpose
Arcimboldophasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Structure summary
  • Version 1.2: 2021-05-05
    Changes: Database references, Derived calculations