3D3K

Crystal structure of human Edc3p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human Edc3 and its functional implications

Ling, S.H.M.Decker, C.J.Walsh, M.A.She, M.Parker, R.Song, H.

(2008) Mol.Cell.Biol. 28: 5965-5976

  • DOI: 10.1128/MCB.00761-08
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Edc3 is an enhancer of decapping and serves as a scaffold that aggregates mRNA ribonucleoproteins together for P-body formation. Edc3 forms a network of interactions with the components of the mRNA decapping machinery and has a modular domain archite ...

    Edc3 is an enhancer of decapping and serves as a scaffold that aggregates mRNA ribonucleoproteins together for P-body formation. Edc3 forms a network of interactions with the components of the mRNA decapping machinery and has a modular domain architecture consisting of an N-terminal Lsm domain, a central FDF domain, and a C-terminal YjeF-N domain. We have determined the crystal structure of the N-terminally truncated human Edc3 at a resolution of 2.2 A. The structure reveals that the YjeF-N domain of Edc3 possesses a divergent Rossmann fold topology that forms a dimer, which is supported by sedimentation velocity and sedimentation equilibrium analysis in solution. The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species. Structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation, and likely for regulating the yeast Rps28B mRNA as well, suggesting that the dimeric form of Edc3 is a structural and functional unit in mRNA degradation.


    Organizational Affiliation

    Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enhancer of mRNA-decapping protein 3
A, B, C, D
259Homo sapiensMutation(s): 0 
Gene Names: EDC3 (LSM16, YJDC, YJEFN2)
Find proteins for Q96F86 (Homo sapiens)
Go to Gene View: EDC3
Go to UniProtKB:  Q96F86
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 94.377α = 90.00
b = 169.204β = 90.00
c = 163.609γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SnBphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-05-12 
  • Released Date: 2008-08-26 
  • Deposition Author(s): Ling, S.H.M.

Revision History 

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance