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: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.235 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1RK8

  • 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 partner of Mago-Y14 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CG8781-PA protein A165Drosophila melanogasterMutation(s): 0 
Gene Names: tsuY14CG8781
Find proteins for Q9V535 (Drosophila melanogaster)
Explore Q9V535 
Go to UniProtKB:  Q9V535
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mago nashi protein B147Drosophila melanogasterMutation(s): 0 
Gene Names: magomgnCG9401
Find proteins for P49028 (Drosophila melanogaster)
Explore P49028 
Go to UniProtKB:  P49028
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Within the bgcn gene intron protein C58Drosophila melanogasterMutation(s): 0 
Gene Names: wibgPymCG30176/CG10330CG30176
Find proteins for P82804 (Drosophila melanogaster)
Explore P82804 
Go to UniProtKB:  P82804
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.357α = 90
b = 106.357β = 90
c = 58.139γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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