Solution structure of CUG-BP2 RRM3 in complex with 5'-UUUAA-3' RNA

Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history


Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination.

Diarra Dit Konte, N.Krepl, M.Damberger, F.F.Ripin, N.Duss, O.Sponer, J.Allain, F.H.

(2017) Nat Commun 8: 654-654

  • DOI: https://doi.org/10.1038/s41467-017-00631-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3' untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5'-UUUAA-3' originating from the COX-2 3'-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications. This study highlights a mechanism for RNA discrimination possibly common to multiple RRMs as several prominent members display a similar rearrangement of aromatic residues upon binding their targets.The RNA Recognition Motif (RRM) is the most ubiquitous RNA binding domain. Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA binding surface exists in different states and that a conformational switch of aromatic side-chains fine-tunes sequence specific binding affinities.

  • Organizational Affiliation

    Department of Biology, ETH Zürich, Institute of Molecular Biology and Biophysics, HPP L 14.1 Hönggerbergring 64, 8093, Zürich, Switzerland.


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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CUGBP Elav-like family member 2114Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for O95319 (Homo sapiens)
Explore O95319 
Go to UniProtKB:  O95319
PHAROS:  O95319
GTEx:  ENSG00000048740 
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UniProt GroupO95319
Sequence Annotations
  • Reference Sequence

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

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other