4BRW

Crystal structure of the yeast Dhh1-Pat1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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:  
    4BRU, 4BRW

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT RNA HELICASE DHH1A377Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DHH1YDL160C
EC: 3.6.4.13
Find proteins for P39517 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39517 
Go to UniProtKB:  P39517
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1B75Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PAT1MRT1YCR077CYCR77C
EC: 3.6.4.13
Find proteins for P25644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25644 
Go to UniProtKB:  P25644
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.635α = 90
b = 105.635β = 90
c = 122.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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