2KF0

NMR structure of U6 ISL at pH 7.0

• PDB DOI:  https://doi.org/10.2210/pdb2KF0/pdb
• NAKB: 2KF0

• Classification: RNA
• Mutation(s): No 


• Deposited: 2009-02-08 Released: 2009-07-21 
• Deposition Author(s): Venditti, V., Butcher, S.E.

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Experimental Data Snapshot

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

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

• PubMed: 19591840 
• DOI: https://doi.org/10.1016/j.jmb.2009.07.003
• Primary Citation of Related Structures:  
  2KEZ, 2KF0


• 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)=6.5). 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.67 kDa 
• Atom Count: 507 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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')	A	24	N/A

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Venditti, V., Butcher, S.E.

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations