1NZ1

Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.

Reiter, N.J., Nikstad, L.J., Allman, A.M., Johnson, R.J., Butcher, S.E.

(2003) RNA 9: 533-542

  • DOI: 10.1261/rna.2199103
  • Primary Citation of Related Structures:  
    1NZ1, 1SY4

  • PubMed Abstract: 

    • Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer ...

    Phosphorothioate-substitution experiments are often used to elucidate functionally important metal ion-binding sites on RNA. All previous experiments with S(P)-phosphorothioate-substituted RNAs have been done in the absence of structural information for this particular diastereomer. Yeast U6 RNA contains a metal ion-binding site that is essential for spliceosome function and includes the pro-S(P) oxygen 5' of U(80). S(P)-phosphorothioate substitution at this location creates spliceosomes dependent on thiophilic ions for the first step of splicing. We have determined the solution structure of the U(80) S(P)-phosphorothioate-substituted U6 intramolecular stem-loop (ISL), and also report the refined NMR structure of the unmodified U6 ISL. Both structures were determined with inclusion of (1)H-(13)C residual dipolar couplings. The precision of the structures with and without phosphorothioate (RMSD = 1.05 and 0.79 A, respectively) allows comparison of the local and long-range structural effect of the modification. We find that the U6-ISL structure is unperturbed by the phosphorothioate. Additionally, the thermodynamic stability of the U6 ISL is dependent on the protonation state of the A(79)-C(67) wobble pair and is not affected by the adjacent phosphorothioate. These results indicate that a single S(P)-phosphorothioate substitution can be structurally benign, and further validate the metal ion rescue experiments used to identify the essential metal-binding site(s) in the spliceosome.

    Organizational Affiliation: 

    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
SP U6 Intramolecular Stem-Loop RNAA 24N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 17 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1NZ1 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations