6S8S

Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2WAX


Literature

Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.

Peter, D.Ruscica, V.Bawankar, P.Weber, R.Helms, S.Valkov, E.Igreja, C.Izaurralde, E.

(2019) Genes Dev 33: 1355-1360

  • DOI: https://doi.org/10.1101/gad.329219.119
  • Primary Citation of Related Structures:  
    6S8R, 6S8S

  • PubMed Abstract: 
  • GIGYF (Grb10-interacting GYF [glycine-tyrosine-phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp-Glu-Ala-Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression ...

    GIGYF (Grb10-interacting GYF [glycine-tyrosine-phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp-Glu-Ala-Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression. However, the underlying molecular mechanism remains unclear. Here, we report that GIGYF contains a motif necessary and sufficient for direct interaction with Me31B/DDX6. A 2.4 Å crystal structure of the GIGYF-Me31B complex reveals that this motif arranges into a coil connected to a β hairpin on binding to conserved hydrophobic patches on the Me31B RecA2 domain. Structure-guided mutants indicate that 4EHP-GIGYF-DDX6 complex assembly is required for tristetraprolin-mediated down-regulation of an AU-rich mRNA, thus revealing the molecular principles of translational repression.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX6
A, C
193Homo sapiensMutation(s): 0 
Gene Names: DDX6HLR2RCK
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P26196 (Homo sapiens)
Explore P26196 
Go to UniProtKB:  P26196
PHAROS:  P26196
Entity Groups  
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UniProt GroupP26196
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Enhancer of mRNA-decapping protein 3
B, D
44Homo sapiensMutation(s): 0 
Gene Names: EDC3LSM16YJDCYJEFN2PP844
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F86 (Homo sapiens)
Explore Q96F86 
Go to UniProtKB:  Q96F86
PHAROS:  Q96F86
Entity Groups  
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UniProt GroupQ96F86
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.425α = 90
b = 47.878β = 96.34
c = 65.757γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references