3iki: Difference between revisions
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New page: '''Unreleased structure''' The entry 3iki is ON HOLD Authors: Sheng, J., Hassan, A.E.A., Zhang, W., Gan, J., Huang, Z. Description: 5-SMe-dU containing DNA octamer ''Page seeded by [h... |
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The | ==5-SMe-dU containing DNA octamer== | ||
<StructureSection load='3iki' size='340' side='right'caption='[[3iki]], [[Resolution|resolution]] 1.38Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3iki]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKI FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.38Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene>, <scene name='pdbligand=US2:2-DEOXY-5-(METHYLSULFANYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>US2</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=3iki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iki OCA], [https://pdbe.org/3iki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iki RCSB], [https://www.ebi.ac.uk/pdbsum/3iki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iki ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH(3)) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH(3) and its 5'-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH(3) is replaced with a larger atom (selenium or sulfur). The 5-O-CH(3) modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH(3) modification, which might potentially rigidify the local conformation and facilitates translation. | |||
Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.,Sheng J, Zhang W, Hassan AE, Gan J, Soares AS, Geng S, Ren Y, Huang Z Nucleic Acids Res. 2012 May 28. PMID:22641848<ref>PMID:22641848</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3iki" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Gan J]] | |||
[[Category: Hassan AEA]] | |||
[[Category: Huang Z]] | |||
[[Category: Sheng J]] | |||
[[Category: Zhang W]] | |||
