7y8p: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 7y8p is ~~ON HOLD until Paper~~ Publication

==Crystal structure of 4'-selenoRNA duplex==

== Structural highlights ==

<table><tr><td colspan='2'>[[7y8p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y8P FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IKS:[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)selenolan-2-yl]methyl+dihydrogen+phosphate'>IKS</scene>, <scene name='pdbligand=ILK:[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)selenolan-2-yl]methyl+dihydrogen+phosphate'>ILK</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=7y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y8p OCA], [https://pdbe.org/7y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y8p RCSB], [https://www.ebi.ac.uk/pdbsum/7y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y8p ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

A large number of chemically modified oligonucleotides (ONs) have been developed for RNA-based technologies. In most modified RNAs, the characteristic 2'-hydroxyl (2'-OH) groups are removed to enhance both nuclease resistance and hybridization ability. However, the importance of the 2'-OH group in RNA structure and function is well known. Here, we report the synthesis and properties of 4'-selenoRNA in which all four nucleoside units retain the 2'-OH groups but contain a selenium atom instead of an oxygen atom at the 4'-position of the furanose ring. 4'-SelenoRNA has enhanced ability to form duplexes with RNA, and high endonuclease resistance despite the presence of the 2'-OH groups. X-ray crystallography analysis showed that the 4'-selenoRNA duplex adopts an A-conformation, similar to natural RNA, although one 4'-selenocytidine residue has unusual South-type sugar puckering. Furthermore, preliminary studies using 4'-seleno-modified siRNAs suggest that 4'-selenoRNA may be applicable to RNA interference technology. Collectively, our results raise the possibility of a new class of modified RNA in which 2'-OH groups do not need to be masked.

~~Authors: Kondo, J., Minakawa~~, N., ~~Ohta,~~ M., Takahashi, H., Tarashima, N.

Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog.,Ota M, Takahashi H, Nogi Y, Kagotani Y, Saito-Tarashima N, Kondo J, Minakawa N Bioorg Med Chem. 2022 Dec 15;76:117093. doi: 10.1016/j.bmc.2022.117093. Epub 2022 , Nov 19. PMID:36434923<ref>PMID:36434923</ref>

~~Description: Crystal structure~~ of ~~4''~~-~~selenoRNA duplex~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Ohta, M~~]]

[[Category: Kondo, J]]

== References ==

[[Category: ~~Takahashi, H~~]]

[[Category: ~~Tarashima, N~~]]

__TOC__

[[Category: ~~Minakawa,~~ N]]

</StructureSection>

[[Category: Large Structures]]

[[Category: Synthetic construct]]

[[Category: Kondo J]]

[[Category: Minakawa N]]

[[Category: Ohta M]]

[[Category: Takahashi H]]

[[Category: Tarashima N]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7y8p is ON HOLD  until Paper Publication
+==Crystal structure of 4'-selenoRNA duplex==
+<StructureSection load='7y8p' size='340' side='right'caption='[[7y8p]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7y8p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y8P FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IKS:[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)selenolan-2-yl]methyl+dihydrogen+phosphate'>IKS</scene>, <scene name='pdbligand=ILK:[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)selenolan-2-yl]methyl+dihydrogen+phosphate'>ILK</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=7y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y8p OCA], [https://pdbe.org/7y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y8p RCSB], [https://www.ebi.ac.uk/pdbsum/7y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y8p ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A large number of chemically modified oligonucleotides (ONs) have been developed for RNA-based technologies. In most modified RNAs, the characteristic 2'-hydroxyl (2'-OH) groups are removed to enhance both nuclease resistance and hybridization ability. However, the importance of the 2'-OH group in RNA structure and function is well known. Here, we report the synthesis and properties of 4'-selenoRNA in which all four nucleoside units retain the 2'-OH groups but contain a selenium atom instead of an oxygen atom at the 4'-position of the furanose ring. 4'-SelenoRNA has enhanced ability to form duplexes with RNA, and high endonuclease resistance despite the presence of the 2'-OH groups. X-ray crystallography analysis showed that the 4'-selenoRNA duplex adopts an A-conformation, similar to natural RNA, although one 4'-selenocytidine residue has unusual South-type sugar puckering. Furthermore, preliminary studies using 4'-seleno-modified siRNAs suggest that 4'-selenoRNA may be applicable to RNA interference technology. Collectively, our results raise the possibility of a new class of modified RNA in which 2'-OH groups do not need to be masked.
-Authors: Kondo, J., Minakawa, N., Ohta, M., Takahashi, H., Tarashima, N.
+Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog.,Ota M, Takahashi H, Nogi Y, Kagotani Y, Saito-Tarashima N, Kondo J, Minakawa N Bioorg Med Chem. 2022 Dec 15;76:117093. doi: 10.1016/j.bmc.2022.117093. Epub 2022 , Nov 19. PMID:36434923<ref>PMID:36434923</ref>
-Description: Crystal structure of 4''-selenoRNA duplex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ohta, M]]
+<div class="pdbe-citations 7y8p" style="background-color:#fffaf0;"></div>
-[[Category: Kondo, J]]
+== References ==
-[[Category: Takahashi, H]]
+<references/>
-[[Category: Tarashima, N]]
+__TOC__
-[[Category: Minakawa, N]]
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Kondo J]]
+[[Category: Minakawa N]]
+[[Category: Ohta M]]
+[[Category: Takahashi H]]
+[[Category: Tarashima N]]