1c4l: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (11 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR== | |||
<StructureSection load='1c4l' size='340' side='right'caption='[[1c4l]]' scene=''> | |||
== Structural highlights == | |||
| | <table><tr><td colspan='2'>[[1c4l]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C4L 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c4l OCA], [https://pdbe.org/1c4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c4l RCSB], [https://www.ebi.ac.uk/pdbsum/1c4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c4l ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
''' | == Publication Abstract from PubMed == | ||
== | |||
The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex. | The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex. | ||
Solution structure of an RNA duplex including a C-U base pair.,Tanaka Y, Kojima C, Yamazaki T, Kodama TS, Yasuno K, Miyashita S, Ono A, Ono A, Kainosho M, Kyogoku Y Biochemistry. 2000 Jun 20;39(24):7074-80. PMID:10852704<ref>PMID:10852704</ref> | |||
Solution structure of an RNA duplex including a C-U base pair., Tanaka Y, Kojima C, Yamazaki T, Kodama TS, Yasuno K, Miyashita S, Ono A, Ono A, Kainosho M, Kyogoku Y | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1c4l" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Kainosho M]] | |||
[[Category: Kodama TS]] | |||
[[Category: Kojima C]] | |||
[[Category: Kyogoku Y]] | |||
[[Category: Miyashita S]] | |||
[[Category: Ono AM]] | |||
[[Category: Ono AS]] | |||
[[Category: Tanaka Y]] | |||
[[Category: Yamazaki T]] | |||
[[Category: Yasuno K]] | |||
Latest revision as of 11:38, 22 November 2023
SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR
| ||||||||||||
