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.


2ygh

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:52, 20 December 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ygh.png|left|200px]]
 
-
<!--
+
==SAM-I riboswitch with a G2nA mutation in the Kink turn in complex with S-adenosylmethionine==
-
The line below this paragraph, containing "STRUCTURE_2ygh", creates the "Structure Box" on the page.
+
<StructureSection load='2ygh' size='340' side='right'caption='[[2ygh]], [[Resolution|resolution]] 2.60&Aring;' 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'>[[2ygh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YGH 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">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-
{{STRUCTURE_2ygh| PDB=2ygh | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ygh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ygh OCA], [https://pdbe.org/2ygh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ygh RCSB], [https://www.ebi.ac.uk/pdbsum/2ygh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ygh ProSAT]</span></td></tr>
 +
</table>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a GA and AG pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.
-
===SAM-I RIBOSWITCH WITH A G2NA MUTATION IN THE KINK TURN IN COMPLEX WITH S-ADENOSYLMETHIONINE===
+
RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn.,Schroeder KT, Daldrop P, Lilley DM Structure. 2011 Sep 7;19(9):1233-40. PMID:21893284<ref>PMID:21893284</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2ygh" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_21893284}}, adds the Publication Abstract to the page
+
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 21893284 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_21893284}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
-
[[2ygh]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YGH OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Daldrop P]]
-
==Reference==
+
[[Category: Lilley D]]
-
<ref group="xtra">PMID:021893284</ref><references group="xtra"/>
+
[[Category: Schroeder K]]
-
[[Category: Daldrop, P.]]
+
-
[[Category: Lilley, D.]]
+
-
[[Category: Schroeder, K.]]
+
-
[[Category: Rna]]
+

Current revision

SAM-I riboswitch with a G2nA mutation in the Kink turn in complex with S-adenosylmethionine

PDB ID 2ygh

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/2ygh"
Personal tools