6F9W

Crystal structure of the LSM domain of LSM14 in complex with a C-terminal peptide of 4E-T

  • Classification: RNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

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: https://doi.org/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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LSM14 homolog AA87Homo sapiensMutation(s): 0 
Gene Names: LSM14A, C19orf13, FAM61A, RAP55, RAP55A
UniProt & NIH Common Fund Data Resources
Find proteins for Q8ND56 (Homo sapiens)
Explore Q8ND56 
Go to UniProtKB:  Q8ND56
PHAROS:  Q8ND56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ND56
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E transporterB37Homo sapiensMutation(s): 1 
Gene Names: EIF4ENIF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRA8 (Homo sapiens)
Explore Q9NRA8 
Go to UniProtKB:  Q9NRA8
PHAROS:  Q9NRA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRA8
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.89α = 90
b = 64.89β = 90
c = 61.67γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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View more in-depth experimental data
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
Natural Sciences and Engineering Research Council of Canada (NSERC)CanadaRGPIN-2014-06434
Natural Sciences and Engineering Research Council of Canada (NSERC)CanadaRGPAS 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