1RK8

Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex

Bono, F.Ebert, J.Unterholzner, L.Guettler, T.Izaurralde, E.Conti, E.

(2004) EMBO Rep. 5: 304-310

  • DOI: 10.1038/sj.embor.7400091

  • PubMed Abstract: 
  • The exon junction complex (EJC) is deposited on mRNAs as a consequence of splicing and influences postsplicing mRNA metabolism. The Mago-Y14 heterodimer is a core component of the EJC. Recently, the protein PYM has been identified as an interacting p ...

    The exon junction complex (EJC) is deposited on mRNAs as a consequence of splicing and influences postsplicing mRNA metabolism. The Mago-Y14 heterodimer is a core component of the EJC. Recently, the protein PYM has been identified as an interacting partner of Mago-Y14. Here we show that PYM is a cytoplasmic RNA-binding protein that is excluded from the nucleus by Crm1. PYM interacts directly with Mago-Y14 by means of its N-terminal domain. The crystal structure of the Drosophila ternary complex at 1.9 A resolution reveals that PYM binds Mago and Y14 simultaneously, capping their heterodimerization interface at conserved surface residues. Formation of this ternary complex is also observed with the human proteins. Mago residues involved in the interaction with PYM have been implicated in nonsense-mediated mRNA decay (NMD). Consistently, human PYM is active in NMD tethering assays. Together, these data suggest a role for PYM in NMD.


    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CG8781-PA protein
A
165Drosophila melanogasterGene Names: tsu (Y14)
Find proteins for Q9V535 (Drosophila melanogaster)
Go to UniProtKB:  Q9V535
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mago nashi protein
B
147Drosophila melanogasterGene Names: mago (mgn)
Find proteins for P49028 (Drosophila melanogaster)
Go to UniProtKB:  P49028
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Within the bgcn gene intron protein
C
58Drosophila melanogasterGene Names: Pym (wibg)
Find proteins for P82804 (Drosophila melanogaster)
Go to UniProtKB:  P82804
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.357α = 90.00
b = 106.357β = 90.00
c = 58.139γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance