The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
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DOI：
10.1016/s0969-2126(00)80033-7
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发表时间：
1999-11-15
期刊：
影响因子：
5.7
通讯作者：
Dumas, P
中科院分区：
文献类型：
--
作者：
Ennifar, E;Yusupov, M;Dumas, P
背景：逆转录病毒复制的一个重要步骤是在衣壳化之前基因组 RNA 的二聚化。二聚化是由瞬时“接吻环复合物”的形成引发的，据信该复合物随后通过核衣壳蛋白（NCp）成熟为延伸的双链体。尽管化学探测和核磁共振波谱已经深入了解了接环结构的结构，但迄今为止还没有关于延伸双链体状态的结构信息。 结果：最小的 HIV-1 RNA 二聚化起始位点的结构已在两个不同的空间群中以 2.3 埃的分辨率解析出来。它揭示了一个 22 个碱基对的扩展双链体，具有两个非典型的 Watson-Crick 样 G-A 错配，每个错配都与凸出的腺嘌呤相邻。该结构在深沟宽度和G-A碱基对构象方面表现出显着的不对称性。清楚地识别出八个镁阳离子的网络，其中一个异常地被极窄的深主沟上每个凸起的 3' 磷酸盐螯合。结论：这些晶体结构代表了初始接吻环复合物的推定成熟形式。他们展示了这种自我互补的 RNA 发夹环获得更稳定的延伸双链结构的能力。两个突出的腺嘌呤形成了一个引人注目的“碱基夹”，可能是一种识别信号，顺式表示另一个病毒 RNA 序列，反式表示蛋白质（可能是 NCp）。镁的结合对于促进和稳定观察到的这些凸起的螺旋外构象可能很重要。
Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far.Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Angstrom resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove.Conclusions: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.