2XEB

NMR STRUCTURE OF THE PROTEIN-UNBOUND SPLICEOSOMAL U4 SNRNA 5' STEM LOOP


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the K-turn U4 RNA: a combined NMR and SANS study.

Falb, M.Amata, I.Gabel, F.Simon, B.Carlomagno, T.

(2010) Nucleic Acids Res 38: 6274-6285

  • DOI: https://doi.org/10.1093/nar/gkq380
  • Primary Citation of Related Structures:  
    2XEB

  • PubMed Abstract: 

    K-turn motifs are universal RNA structural elements providing a binding platform for proteins in several cellular contexts. Their characteristic is a sharp kink in the phosphate backbone that puts the two helical stems of the protein-bound RNA at an angle of 60°. However, to date no high-resolution structure of a naked K-turn motif is available. Here, we present the first structural investigation at atomic resolution of an unbound K-turn RNA (the spliceosomal U4-Kt RNA) by a combination of NMR and small-angle neutron scattering data. With this study, we wish to address the question whether the K-turn structural motif assumes the sharply kinked conformation in the absence of protein binders and divalent cations. Previous studies have addressed this question by fluorescence resonance energy transfer, biochemical assays and molecular dynamics simulations, suggesting that the K-turn RNAs exist in equilibrium between a kinked conformation, which is competent for protein binding, and a more extended conformation, with the population distribution depending on the concentration of divalent cations. Our data shows that the U4-Kt RNA predominantly assumes the more extended conformation in the absence of proteins and divalent cations. The internal loop region is well structured but adopts a different conformation from the one observed in complex with proteins. Our data suggests that the K-turn consensus sequence does not per se code for the kinked conformation; instead the sharp backbone kink requires to be stabilized by protein binders.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, D-69117 Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP* GP*GP*UP*U)-3'19Homo sapiens
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3'14Homo sapiens
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Database references
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Other