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1tbk

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[[Image:1tbk.gif|left|200px]]
 
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{{Structure
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==NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.==
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|PDB= 1tbk |SIZE=350|CAPTION= <scene name='initialview01'>1tbk</scene>
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<StructureSection load='1tbk' size='340' side='right'caption='[[1tbk]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<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 [https://proteopedia.org/fgij/fg.htm?mol=1TBK FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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|GENE=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tbk OCA], [https://pdbe.org/1tbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tbk RCSB], [https://www.ebi.ac.uk/pdbsum/1tbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tbk ProSAT]</span></td></tr>
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}}
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</table>
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<div style="background-color:#fffaf0;">
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'''NMR structure of the VS ribozyme stem-loop V RNA in the absence of multivalent ions.'''
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== Publication Abstract from PubMed ==
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==Overview==
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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.
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.
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==About this Structure==
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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>
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1TBK is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TBK OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15766243 15766243]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1tbk" style="background-color:#fffaf0;"></div>
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[[Category: Campbell, D O.]]
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[[Category: Legault, P.]]
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[[Category: u-turn; hairpin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:16:18 2008''
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==See Also==
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Campbell DO]]
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[[Category: Legault P]]

Current revision

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

PDB ID 1tbk

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