2dd3: Difference between revisions

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{{Seed}}
[[Image:2dd3.png|left|200px]]


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==An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack==
The line below this paragraph, containing "STRUCTURE_2dd3", creates the "Structure Box" on the page.
<StructureSection load='2dd3' size='340' side='right'caption='[[2dd3]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
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<table><tr><td colspan='2'>[[2dd3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD3 FirstGlance]. <br>
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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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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene></td></tr>
{{STRUCTURE_2dd3|  PDB=2dd3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd3 OCA], [https://pdbe.org/2dd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd3 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.


===An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack===
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.,Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425<ref>PMID:16734425</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_16734425}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2dd3" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16734425 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16734425}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2DD3 is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA].
[[Category: Chen G]]
 
[[Category: Kennedy SD]]
==Reference==
[[Category: Krugh TR]]
<ref group="xtra">PMID:16734425</ref><references group="xtra"/>
[[Category: Turner DH]]
[[Category: Chen, G.]]
[[Category: Kennedy, S D.]]
[[Category: Krugh, T R.]]
[[Category: Turner, D H.]]
[[Category: Alternating sheared aa pair]]
[[Category: Kink-turn motif]]
[[Category: Rapid conformation exchange]]
[[Category: Rna secondary structure prediction]]
[[Category: Sequence specific a-minor motif]]
[[Category: Thermodynamic]]
 
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Latest revision as of 16:34, 13 December 2023

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack

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