2KF0

NMR structure of U6 ISL at pH 7.0


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.

Venditti, V.Clos, L.Niccolai, N.Butcher, S.E.

(2009) J Mol Biol 391: 894-905

  • DOI: 10.1016/j.jmb.2009.07.003
  • Primary Citation of Related Structures:  
    2KF0, 2KEZ

  • PubMed Abstract: 
  • The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6 ...

    The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption of the protonated C-A(+) pair and formation of a new C-U pair, which explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix.


    Related Citations: 
    • Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
      Reiter, N.J., Nikstad, L.J., Allmann, A.M., Johnson, R.J., Butcher, S.E.
      (2003) RNA 9: 533
    • Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change.
      Reiter, N.J., Blad, H., Abildgaard, F., Butcher, S.E.
      (2004) Biochemistry 43: 13739

    Organizational Affiliation

    Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, Italy.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP*GP*AP*AP*CP*C)-3')A24N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 12 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2KF0 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance