Crystal Structure of S. pombe Pdc1 Ge1 Domain

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery.

Fromm, S.A.Kamenz, J.Noldeke, E.R.Neu, A.Zocher, G.Sprangers, R.

(2014) Angew Chem Int Ed Engl 53: 7354-7359

  • DOI: https://doi.org/10.1002/anie.201402885
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In eukaryotic cells, components of the 5' to 3' mRNA degradation machinery can undergo a rapid phase transition. The resulting cytoplasmic foci are referred to as processing bodies (P-bodies). The molecular details of the self-aggregation process are, however, largely undetermined. Herein, we use a bottom-up approach that combines NMR spectroscopy, isothermal titration calorimetry, X-ray crystallography, and fluorescence microscopy to probe if mRNA degradation factors can undergo phase transitions in vitro. We show that the Schizosaccharomyces pombe Dcp2 mRNA decapping enzyme, its prime activator Dcp1, and the scaffolding proteins Edc3 and Pdc1 are sufficient to reconstitute a phase-separation process. Intermolecular interactions between the Edc3 LSm domain and at least 10 helical leucine-rich motifs in Dcp2 and Pdc1 build the core of the interaction network. We show that blocking of these interactions interferes with the clustering behavior, both in vitro and in vivo.

  • Organizational Affiliation

    Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen (Germany).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PDC1 GE1 DOMAIN143Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: SPAC20G4.08SPAC4F10.01
Find proteins for O13892 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13892 
Go to UniProtKB:  O13892
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13892
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.33α = 90
b = 77.84β = 90
c = 36.51γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references