2l8f: Difference between revisions

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[[Image:2l8f.jpg|left|200px]]


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==Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon==
The line below this paragraph, containing "STRUCTURE_2l8f", creates the "Structure Box" on the page.
<StructureSection load='2l8f' size='340' side='right'caption='[[2l8f]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2l8f]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L8F FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2l8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l8f OCA], [https://pdbe.org/2l8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l8f RCSB], [https://www.ebi.ac.uk/pdbsum/2l8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l8f ProSAT]</span></td></tr>
{{STRUCTURE_2l8f|  PDB=2l8f  |  SCENE=  }}
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 x 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37 degrees C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.


===Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon===
NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.,Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH RNA. 2011 Sep;17(9):1664-77. Epub 2011 Jul 21. PMID:21778280<ref>PMID:21778280</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_21778280}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2l8f" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 21778280 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_21778280}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2l8f]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L8F OCA].
[[Category: Kennedy SD]]
 
[[Category: Lerman Y]]
==Reference==
[[Category: Turner DH]]
<ref group="xtra">PMID:021778280</ref><references group="xtra"/>
[[Category: Kennedy, S D.]]
[[Category: Lerman, Y.]]
[[Category: Turner, D H.]]
[[Category: 3rr]]
[[Category: Internal loop]]
[[Category: Rna]]
[[Category: Rna motif]]

Latest revision as of 05:39, 15 May 2024

Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon

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