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

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  • Alister Burt
  • Lorenzo Gaifas
  • Tom Dendooven
  • Irina Gutsche

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.

Suggested Citation

  • Alister Burt & Lorenzo Gaifas & Tom Dendooven & Irina Gutsche, 2021. "A flexible framework for multi-particle refinement in cryo-electron tomography," PLOS Biology, Public Library of Science, vol. 19(8), pages 1-16, August.
    • Handle: RePEc:plo:pbio00:3001319
    DOI: 10.1371/journal.pbio.3001319
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    1. Takanori Nakane & Abhay Kotecha & Andrija Sente & Greg McMullan & Simonas Masiulis & Patricia M. G. E. Brown & Ioana T. Grigoras & Lina Malinauskaite & Tomas Malinauskas & Jonas Miehling & Tomasz Ucha, 2020. "Single-particle cryo-EM at atomic resolution," Nature, Nature, vol. 587(7832), pages 152-156, November.
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