1tbk: Difference between revisions

Line 1:

[[~~Image~~:1tbk.~~png|left|200px~~]]

==NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.==

== Structural highlights ==

<table><tr><td colspan='2'>[[1tbk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TBK FirstGlance]. <br>

</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tbk RCSB], [http://www.ebi.ac.uk/pdbsum/1tbk PDBsum]</span></td></tr>

<table>

== Publication Abstract from PubMed ==

An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.

~~{{STRUCTURE_1tbk| PDB=1tbk | SCENE= }}~~

Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping.,Campbell DO, Legault P Biochemistry. 2005 Mar 22;44(11):4157-70. PMID:15766243<ref>PMID:15766243</ref>

~~===NMR structure~~ of the ~~VS ribozyme stem-loop V RNA in the absence~~ of ~~multivalent ions~~.~~===~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

~~{{ABSTRACT_PUBMED_15766243}}~~

~~==About this Structure==~~

~~[[1tbk]] is a 1 chain structure. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA].~~

==See Also==

*[[Ribozyme|Ribozyme]]

== References ==

==~~Reference~~==

<~~ref group="xtra">PMID:015766243<~~/~~ref~~><~~references group="xtra"~~/>

__TOC__

</StructureSection>

[[Category: Campbell, D O.]]

[[Category: Legault, P.]]

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@@ Line 1: / Line 1: @@
-[[Image:1tbk.png|left|200px]]
+==NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.==
+<StructureSection load='1tbk' size='340' side='right' caption='[[1tbk]], [[NMR_Ensembles_of_Models | 11 NMR models]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1tbk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TBK FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tbk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tbk RCSB], [http://www.ebi.ac.uk/pdbsum/1tbk PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.
-{{STRUCTURE_1tbk|  PDB=1tbk  |  SCENE=  }}
+Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping.,Campbell DO, Legault P Biochemistry. 2005 Mar 22;44(11):4157-70. PMID:15766243<ref>PMID:15766243</ref>
-===NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_15766243}}
-==About this Structure==
-[[1tbk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA].
 ==See Also==
 *[[Ribozyme|Ribozyme]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015766243</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Campbell, D O.]]
 [[Category: Legault, P.]]