The solution structure of hsDND1 RRM12 bound to CUUAUUUG RNA

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations and lowest energy 

wwPDB Validation   3D Report Full Report

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The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation.

Duszczyk, M.M.Wischnewski, H.Kazeeva, T.Arora, R.Loughlin, F.E.von Schroetter, C.Pradere, U.Hall, J.Ciaudo, C.Allain, F.H.

(2022) Nat Commun 13: 5892-5892

  • DOI: https://doi.org/10.1038/s41467-022-33552-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1's tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unusual mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1's double-stranded RNA binding domain (dsRBD), which is dispensable for binding of a subset of targets in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation.

  • Organizational Affiliation

    Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dead end protein homolog 1227Homo sapiensMutation(s): 0 
Gene Names: DND1RBMS4
Find proteins for Q8IYX4 (Homo sapiens)
Explore Q8IYX4 
Go to UniProtKB:  Q8IYX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IYX4
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*UP*UP*AP*UP*UP*UP*G)-3')8Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations and lowest energy 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_149921
Swiss National Science FoundationSwitzerland31003A_170130

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references