A flexible framework for multi-particle refinement in cryo-electron tomography

Alister Burt, Lorenzo Gaifas, Tom Dendooven and Irina Gutsche

PLOS Biology, 2021, vol. 19, issue 8, 1-16

Abstract: 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.Employing optimal computational methodology in cryo-electron tomography is not always easy; this article provides a set of tools and a complete guide to obtaining high-resolution structures from cryo-ET data.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pbio00:3001319

DOI: 10.1371/journal.pbio.3001319

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