6F9S

Crystal structure of the C-terminal RecA domain of DDX6 in complex with a conserved peptide from LSM14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes.

Brandmann, T.Fakim, H.Padamsi, Z.Youn, J.Y.Gingras, A.C.Fabian, M.R.Jinek, M.

(2018) EMBO J. 37: --

  • DOI: 10.15252/embj.201797869
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-bo ...

    The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6. LSM14 binds DDX6 via a unique non-contiguous motif with distinct directionality as compared to other DDX6-interacting proteins. Together with mutational and proteomic studies, the LSM14-DDX6 structure reveals that LSM14 has adopted a divergent mode of binding DDX6 in order to support the formation of mRNA silencing complexes and P-body assembly.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent RNA helicase DDX6
A
172Homo sapiensMutation(s): 0 
Gene Names: DDX6 (HLR2, RCK)
EC: 3.6.4.13
Find proteins for P26196 (Homo sapiens)
Go to Gene View: DDX6
Go to UniProtKB:  P26196
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytokinesis, Apoptosis, RNA-associated
B
90Caenorhabditis elegansMutation(s): 0 
Gene Names: car-1
Find proteins for Q9XW17 (Caenorhabditis elegans)
Go to UniProtKB:  Q9XW17
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.148α = 90.00
b = 92.148β = 90.00
c = 149.896γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilSwitzerlandERC-StG-337284
Canadian Institutes of Health Research (CIHR)CanadaMOP-130425
Natural Sciences and Engineering Research Council of Canada (NSERC)CanadaRGPIN-2015-03712
NSERC Discovery and Accelerator SupplementCanadaRGPIN-2014-06434
NSERC Discovery and Accelerator SupplementCanadaRGPAS 462169

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references