Center for Computational Science and Engineering, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan; Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
Center for Computational Science and Engineering, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan; Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
Structure. 2009 Dec 9;17(12):1605-1613. doi: 10.1016/j.str.2009.09.017.
Many three-dimensional density maps of 70S ribosome at various functional states are available now in the Electron Microscopy DataBank at EBI. We used our new flexible-fitting approach to systematically analyze these maps to reveal the global conformational differences between the EM structures. Large-scale ratchet-like deformations were observed in an EM structure of the initiation complex and in some EM structures bound with EFG, RF3, and RRF. In most of them, the L1 stalk, which interacts with the tRNA molecule at the E site of ribosome and is considered to be involved in the release of the tRNA, was in "the blocking state" for the E-tRNA. Furthermore, we found that the EM structures bound with EFG or RRF were aligned in the conformational space, suggesting that the large-scale conformational changes of the 70S ribosome bound with these factors occur along a specific pathway in a concerted manner.
现在，电子显微镜数据库（EBI 的 EMDB）中提供了许多处于不同功能状态的 70S 核糖体的三维密度图。我们使用新的灵活拟合方法系统地分析这些图谱，以揭示 EM 结构之间的全局构象差异。在起始复合物的 EM 结构和与 EFG、RF3 和 RRF 结合的一些 EM 结构中观察到了大规模的棘轮式变形。在其中的大多数结构中，与核糖体 E 位上的 tRNA 分子相互作用的 L1 茎在 E-tRNA 中处于“阻塞状态”。此外，我们发现与 EFG 或 RRF 结合的 EM 结构在构象空间中对齐，表明与这些因子结合的 70S 核糖体的大规模构象变化沿着特定的途径协同发生。
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