4BRU

Crystal structure of the yeast Dhh1-Edc3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of the Yeast Dhh1-Pat1 Complex Reveals How Dhh1 Engages Pat1, Edc3 and RNA in Mutually Exclusive Interactions

Sharif, H.Ozgur, S.Sharma, K.Basquin, C.Urlaub, H.Conti, E.

(2013) Nucleic Acids Res. 41: 8377

  • DOI: 10.1093/nar/gkt600
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5' cap structure is a crucial step that commits deadenylated mRNAs ...

    Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5' cap structure is a crucial step that commits deadenylated mRNAs to 5'-to-3' degradation. Pat1, Edc3 and the DEAD-box protein Dhh1 are evolutionary conserved factors known to participate in both translational repression and decapping, but their interplay is currently unclear. We report the 2.8 Å resolution structure of yeast Dhh1 bound to the N-terminal domain of Pat1. The structure shows how Pat1 wraps around the C-terminal RecA domain of Dhh1, docking onto the Phe-Asp-Phe (FDF) binding site. The FDF-binding site of Dhh1 also recognizes Edc3, revealing why the binding of Pat1 and Edc3 on Dhh1 are mutually exclusive events. Using co-immunoprecipitation assays and structure-based mutants, we demonstrate that the mode of Dhh1-Pat1 recognition is conserved in humans. Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1. Mapping the RNA-binding sites on Dhh1 with a crosslinking-mass spectrometry approach shows a large RNA-binding surface around the C-terminal RecA domain, including the FDF-binding pocket. The results suggest a model for how Dhh1-containing messenger ribonucleoprotein particles might be remodeled upon Pat1 and Edc3 binding.


    Organizational Affiliation

    Structural Cell Biology Department, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, D-82152 Germany and Cellular Biochemistry Department, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-DEPENDENT RNA HELICASE DHH1
A
377Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: DHH1
EC: 3.6.4.13
Find proteins for P39517 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENHANCER OF MRNA-DECAPPING PROTEIN 3
B
43Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EDC3 (LSM16)
Find proteins for P39998 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: EDC3
Go to UniProtKB:  P39998
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.245 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.831α = 90.00
b = 105.831β = 90.00
c = 124.648γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references