2d1b: Difference between revisions
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== | ==Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer== | ||
Dimer formation of HIV-1 genomic RNA through its dimerization initiation | <StructureSection load='2d1b' size='340' side='right'caption='[[2d1b]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2d1b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1B 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=2d1b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1b OCA], [https://pdbe.org/2d1b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1b RCSB], [https://www.ebi.ac.uk/pdbsum/2d1b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1b ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Dimer formation of HIV-1 genomic RNA through its dimerization initiation site (DIS) is crucial to maintaining infectivity. Two types of dimers, the initially generated kissing-loop dimer and the subsequent product of the extended-duplex dimer, are formed in the stem-bulge-stem region with a loop including a self-complementary sequence. NMR chemical shift analysis of a 39mer RNA corresponding to DIS, DIS39, in the kissing-loop and extended-duplex dimers revealed that the three dimensional structures of the stem-bulge-stem region are extremely similar between the two types of dimers. Therefore, we designed two shorter RNA molecules, loop25 and bulge34, corresponding to the loop-stem region and the stem-bulge-stem region of DIS39, respectively. Based upon the chemical shift analysis, the conformation of the loop region of loop25 is identical to that of DIS39 for each of the two types of dimers. The conformation of bulge34 was also found to be the same as that of the corresponding region of DIS39. Thus, we determined the solution structures of loop25 in each of the two types of dimers as well as that of bulge34. Finally, the solution structures of DIS39 in the kissing-loop and extended-duplex dimers were determined by combining the parts of the structures. The solution structures of the two types of dimers were similar to each other in general with a difference found only in the A16 residue. The elucidation of the structures of DIS39 is important to understanding the molecular mechanism of the conformational dynamics of viral RNA molecules. | |||
Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.,Baba S, Takahashi K, Noguchi S, Takaku H, Koyanagi Y, Yamamoto N, Kawai G J Biochem. 2005 Nov;138(5):583-92. PMID:16272570<ref>PMID:16272570</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2d1b" style="background-color:#fffaf0;"></div> | ||
[[Category: Baba | == References == | ||
[[Category: Kawai | <references/> | ||
[[Category: Koyanagi | __TOC__ | ||
[[Category: Noguchi | </StructureSection> | ||
[[Category: Takahashi | [[Category: Human immunodeficiency virus 1]] | ||
[[Category: Takaku | [[Category: Large Structures]] | ||
[[Category: Yamamoto | [[Category: Baba S]] | ||
[[Category: Kawai G]] | |||
[[Category: Koyanagi Y]] | |||
[[Category: Noguchi S]] | |||
[[Category: Takahashi K]] | |||
[[Category: Takaku H]] | |||
[[Category: Yamamoto N]] | |||
Latest revision as of 19:34, 13 December 2023
Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimerSolution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer
Structural highlights
Publication Abstract from PubMedDimer formation of HIV-1 genomic RNA through its dimerization initiation site (DIS) is crucial to maintaining infectivity. Two types of dimers, the initially generated kissing-loop dimer and the subsequent product of the extended-duplex dimer, are formed in the stem-bulge-stem region with a loop including a self-complementary sequence. NMR chemical shift analysis of a 39mer RNA corresponding to DIS, DIS39, in the kissing-loop and extended-duplex dimers revealed that the three dimensional structures of the stem-bulge-stem region are extremely similar between the two types of dimers. Therefore, we designed two shorter RNA molecules, loop25 and bulge34, corresponding to the loop-stem region and the stem-bulge-stem region of DIS39, respectively. Based upon the chemical shift analysis, the conformation of the loop region of loop25 is identical to that of DIS39 for each of the two types of dimers. The conformation of bulge34 was also found to be the same as that of the corresponding region of DIS39. Thus, we determined the solution structures of loop25 in each of the two types of dimers as well as that of bulge34. Finally, the solution structures of DIS39 in the kissing-loop and extended-duplex dimers were determined by combining the parts of the structures. The solution structures of the two types of dimers were similar to each other in general with a difference found only in the A16 residue. The elucidation of the structures of DIS39 is important to understanding the molecular mechanism of the conformational dynamics of viral RNA molecules. Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers.,Baba S, Takahashi K, Noguchi S, Takaku H, Koyanagi Y, Yamamoto N, Kawai G J Biochem. 2005 Nov;138(5):583-92. PMID:16272570[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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