2D1A
Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer
Summary for 2D1A
| Entry DOI | 10.2210/pdb2d1a/pdb |
| Related | 2D17 2D18 2D19 2D1B |
| Descriptor | RNA (1 entity in total) |
| Functional Keywords | dis, hiv-1, rna |
| Total number of polymer chains | 2 |
| Total formula weight | 25309.21 |
| Authors | Baba, S.,Takahashi, K.,Noguchi, S.,Takaku, H.,Koyanagi, Y.,Yamamoto, N.,Kawai, G. (deposition date: 2005-08-15, release date: 2005-11-01, Last modification date: 2024-05-29) |
| Primary citation | Baba, S.,Takahashi, K.,Noguchi, S.,Takaku, H.,Koyanagi, Y.,Yamamoto, N.,Kawai, G. Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138:583-592, 2005 Cited by PubMed Abstract: 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. PubMed: 16272570DOI: 10.1093/jb/mvi158 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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