6F9S

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

  • Classification: RNA
  • Organism(s): Homo sapiens, Caenorhabditis elegans
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2017-12-15 Released: 2018-03-21 
  • Deposition Author(s): Jinek, M., Brandmann, T.
  • Funding Organization(s): European Research Council, Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council of Canada (NSERC), NSERC Discovery and Accelerator Supplement

Experimental Data Snapshot

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

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:  
    6F9S, 6F9W

  • 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-box helicase DDX6, is poorly understood ...

    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 marc.fabian@mcgill.ca jinek@bioc.uzh.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX6A172Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokinesis, Apoptosis, RNA-associatedB90Caenorhabditis elegansMutation(s): 0 
Gene Names: car-1CELE_Y18D10A.17Y18D10A.17
UniProt
Find proteins for Q9XW17 (Caenorhabditis elegans)
Explore Q9XW17 
Go to UniProtKB:  Q9XW17
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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 
  • R-Value Observed: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.148α = 90
b = 92.148β = 90
c = 149.896γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report




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  (Full details and data files)

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