1sy4
From Proteopedia
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|PDB= 1sy4 |SIZE=350|CAPTION= <scene name='initialview01'>1sy4</scene> | |PDB= 1sy4 |SIZE=350|CAPTION= <scene name='initialview01'>1sy4</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1lc6|1LC6]], [[1nz1|1NZ1]], [[1nc0|1NC0]], [[1syz|1SYZ]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sy4 OCA], [http://www.ebi.ac.uk/pdbsum/1sy4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1sy4 RCSB]</span> | ||
}} | }} | ||
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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 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:48:33 2008'' |
Revision as of 20:48, 30 March 2008
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| Ligands: | , , , | ||||||
| Related: | 1LC6, 1NZ1, 1NC0, 1SYZ
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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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