1OO0

Crystal structure of the Drosophila Mago nashi-Y14 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the Drosophila Mago nashi-Y14 complex

Shi, H.Xu, R.M.

(2003) Genes Dev 17: 971-976

  • DOI: https://doi.org/10.1101/gad.260403
  • Primary Citation of Related Structures:  
    1OO0

  • PubMed Abstract: 

    Pre-mRNA splicing is essential for generating mature mRNA and is also important for subsequent mRNA export and quality control. The splicing history is imprinted on spliced mRNA through the deposition of a splicing-dependent multiprotein complex, the exon junction complex (EJC), at approximately 20 nucleotides upstream of exon-exon junctions. The EJC is a dynamic structure containing proteins functioning in the nuclear export and nonsense-mediated decay of spliced mRNAs. Mago nashi (Mago) and Y14 are core components of the EJC, and they form a stable heterodimer that strongly associates with spliced mRNA. Here we report a 1.85 A-resolution structure of the Drosophila Mago-Y14 complex. Surprisingly, the structure shows that the canonical RNA-binding surface of the Y14 RNA recognition motif (RRM) is involved in extensive protein-protein interactions with Mago. This unexpected finding provides important insights for understanding the molecular mechanisms of EJC assembly and RRM-mediated protein-protein interactions.


  • Organizational Affiliation

    W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, New York 11724, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mago nashi protein147Drosophila melanogasterMutation(s): 0 
Gene Names: MAGO
UniProt
Find proteins for P49028 (Drosophila melanogaster)
Explore P49028 
Go to UniProtKB:  P49028
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49028
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CG8781-PA110Drosophila melanogasterMutation(s): 0 
Gene Names: TSU
UniProt
Find proteins for Q9V535 (Drosophila melanogaster)
Explore Q9V535 
Go to UniProtKB:  Q9V535
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V535
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
SR
Query on SR

Download Ideal Coordinates CCD File 
C [auth A]STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.027α = 90
b = 52.387β = 104.9
c = 52.862γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations