This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2ap0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2ap0" [edit=sysop:move=sysop])
Current revision (16:32, 13 December 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ap0.png|left|200px]]
 
-
{{STRUCTURE_2ap0| PDB=2ap0 | SCENE= }}
+
==Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures==
 +
<StructureSection load='2ap0' size='340' side='right'caption='[[2ap0]]' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2ap0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AP0 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5-MONOPHOSPHATE'>CH</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ap0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ap0 OCA], [https://pdbe.org/2ap0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ap0 RCSB], [https://www.ebi.ac.uk/pdbsum/2ap0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ap0 ProSAT]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots.
-
===Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures===
+
The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical.,Cornish PV, Stammler SN, Giedroc DP RNA. 2006 Nov;12(11):1959-69. Epub 2006 Sep 25. PMID:17000902<ref>PMID:17000902</ref>
-
{{ABSTRACT_PUBMED_17000902}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2ap0" style="background-color:#fffaf0;"></div>
-
[[2ap0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AP0 OCA].
+
== References ==
-
 
+
<references/>
-
==Reference==
+
__TOC__
-
<ref group="xtra">PMID:017000902</ref><references group="xtra"/>
+
</StructureSection>
-
[[Category: Cornish, P V.]]
+
[[Category: Large Structures]]
-
[[Category: Giedroc, D P.]]
+
[[Category: Cornish PV]]
-
[[Category: Frameshifting]]
+
[[Category: Giedroc DP]]
-
[[Category: Rna]]
+
-
[[Category: Rna pseudoknot]]
+

Current revision

Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, 20 Lowest Energy Structures

PDB ID 2ap0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ap0"
Personal tools