5J3Y

Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.

Valkov, E.Muthukumar, S.Chang, C.T.Jonas, S.Weichenrieder, O.Izaurralde, E.

(2016) Nat Struct Mol Biol 23: 574-579

  • DOI: https://doi.org/10.1038/nsmb.3232
  • Primary Citation of Related Structures:  
    5J3Q, 5J3T, 5J3Y

  • PubMed Abstract: 

    The removal of the mRNA 5' cap (decapping) by Dcp2 shuts down translation and commits mRNA to full degradation. Dcp2 activity is enhanced by activator proteins such as Dcp1 and Edc1. However, owing to conformational flexibility, the active conformation of Dcp2 and the mechanism of decapping activation have remained unknown. Here, we report a 1.6-Å-resolution crystal structure of the Schizosaccharomyces pombe Dcp2-Dcp1 heterodimer in an unprecedented conformation that is tied together by an intrinsically disordered peptide from Edc1. In this ternary complex, an unforeseen rotation of the Dcp2 catalytic domain allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding, thus explaining decapping activation by increased substrate affinity. The architecture of the Dcp2-Dcp1-Edc1 complex provides a rationale for the conservation of a sequence motif in Edc1 that is also present in unrelated decapping activators, thus indicating that the presently described mechanism of decapping activation is evolutionarily conserved.


  • Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA-decapping enzyme subunit 1
A, C
130Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dcp1SPBC3B9.21
UniProt
Find proteins for Q9P805 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9P805 
Go to UniProtKB:  Q9P805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P805
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA decapping complex subunit 2
B, D
242Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dcp2SPAC19A8.12
EC: 3.6.1.62 (PDB Primary Data), 3 (UniProt)
UniProt
Find proteins for O13828 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13828 
Go to UniProtKB:  O13828
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13828
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.362α = 90
b = 124.362β = 90
c = 366.978γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description