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PDBsum entry 2d17
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References listed in PDB file
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Key reference
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Title
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Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-Loop and extended-Duplex dimers.
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Authors
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S.Baba,
K.Takahashi,
S.Noguchi,
H.Takaku,
Y.Koyanagi,
N.Yamamoto,
G.Kawai.
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Ref.
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J Biochem (tokyo), 2005,
138,
583-592.
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PubMed id
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Abstract
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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.
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Headers
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