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A flexible framework for multi-particle refinement in cryo-electron tomography.
PLOS Biology ( IF 9.8 ) Pub Date : 2021-08-26 , DOI: 10.1371/journal.pbio.3001319
Alister Burt 1 , Lorenzo Gaifas 1 , Tom Dendooven 2 , Irina Gutsche 1
Affiliation  

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are increasingly used for macromolecular structure determination in situ. Here, we introduce a set of computational tools and resources designed to enable flexible approaches to STA through increased automation and simplified metadata handling. We create a bidirectional interface between the Dynamo software package and the Warp-Relion-M pipeline, providing a framework for ab initio and geometrical approaches to multiparticle refinement in M. We illustrate the power of working within this framework by applying it to EMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles (VLPs), and a challenging in situ dataset containing chemosensory arrays in bacterial minicells. Additionally, we provide a comprehensive, step-by-step guide to obtaining a 3.4-Å reconstruction from EMPIAR-10164. The guide is hosted on https://teamtomo.org/, a collaborative online platform we establish for sharing knowledge about cryo-ET.

中文翻译:

用于冷冻电子断层扫描中多粒子细化的灵活框架。

冷冻电子断层扫描 (cryo-ET) 和 subtomogram 平均 (STA) 越来越多地用于原位大分子结构测定。在这里,我们介绍了一组计算工具和资源,旨在通过提高自动化和简化元数据处理实现灵活的 STA 方法。我们在 Dynamo 软件包和 Warp-Relion-M 管道之间创建了一个双向接口,为 M 中多粒子细化的 ab initio 和几何方法提供了一个框架。我们通过将其应用于 EMPIAR-10164 来说明在该框架内工作的力量,包含未成熟 HIV-1 病毒样颗粒 (VLP) 的公开数据集,以及包含细菌微细胞化学感应阵列的具有挑战性的原位数据集。此外,我们还提供了一份全面的分步指南,以帮助您获得 3. 来自 EMPIAR-10164 的 4-Å 重建。该指南托管在 https://teamtomo.org/ 上,这是我们建立的一个协作在线平台,用于共享有关 cryo-ET 的知识。
更新日期:2021-08-26
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