1sy4: Difference between revisions
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[[Image:1sy4.gif|left|200px]] | [[Image:1sy4.gif|left|200px]] | ||
'''Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)''' | {{Structure | ||
|PDB= 1sy4 |SIZE=350|CAPTION= <scene name='initialview01'>1sy4</scene> | |||
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'''Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1SY4 is a [ | 1SY4 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure supersedes the now removed PDB entry 1NYZ. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY4 OCA]. | ||
==Reference== | ==Reference== | ||
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:[http:// | Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12702812 12702812] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Allman, A M.]] | [[Category: Allman, A M.]] | ||
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[[Category: stem-loop (gnra-like tetraloop)]] | [[Category: stem-loop (gnra-like tetraloop)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:11:10 2008'' | ||
Revision as of 12:11, 20 March 2008
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Refined solution structure of the S. cerevisiae U6 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR COUPLINGS (RDCS)
Overview
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.
About this Structure
1SY4 is a Protein complex structure of sequences from [1]. This structure supersedes the now removed PDB entry 1NYZ. Full crystallographic information is available from OCA.
Reference
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification., Reiter NJ, Nikstad LJ, Allmann AM, Johnson RJ, Butcher SE, RNA. 2003 May;9(5):533-42. PMID:12702812
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