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

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 metadat...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Alister Burt, Lorenzo Gaifas, Tom Dendooven, Irina Gutsche
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/cdb855dd7afc4421bb4c555c109637b7
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:cdb855dd7afc4421bb4c555c109637b7
record_format	dspace
spelling	oai:doaj.org-article:cdb855dd7afc4421bb4c555c109637b72021-12-02T19:54:38ZA flexible framework for multi-particle refinement in cryo-electron tomography.1544-91731545-788510.1371/journal.pbio.3001319https://doaj.org/article/cdb855dd7afc4421bb4c555c109637b72021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001319https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Cryo-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.Alister BurtLorenzo GaifasTom DendoovenIrina GutschePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 8, p e3001319 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Alister Burt Lorenzo Gaifas Tom Dendooven Irina Gutsche A flexible framework for multi-particle refinement in cryo-electron tomography.
description	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.
format	article
author	Alister Burt Lorenzo Gaifas Tom Dendooven Irina Gutsche
author_facet	Alister Burt Lorenzo Gaifas Tom Dendooven Irina Gutsche
author_sort	Alister Burt
title	A flexible framework for multi-particle refinement in cryo-electron tomography.
title_short	A flexible framework for multi-particle refinement in cryo-electron tomography.
title_full	A flexible framework for multi-particle refinement in cryo-electron tomography.
title_fullStr	A flexible framework for multi-particle refinement in cryo-electron tomography.
title_full_unstemmed	A flexible framework for multi-particle refinement in cryo-electron tomography.
title_sort	flexible framework for multi-particle refinement in cryo-electron tomography.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/cdb855dd7afc4421bb4c555c109637b7
work_keys_str_mv	AT alisterburt aflexibleframeworkformultiparticlerefinementincryoelectrontomography AT lorenzogaifas aflexibleframeworkformultiparticlerefinementincryoelectrontomography AT tomdendooven aflexibleframeworkformultiparticlerefinementincryoelectrontomography AT irinagutsche aflexibleframeworkformultiparticlerefinementincryoelectrontomography AT alisterburt flexibleframeworkformultiparticlerefinementincryoelectrontomography AT lorenzogaifas flexibleframeworkformultiparticlerefinementincryoelectrontomography AT tomdendooven flexibleframeworkformultiparticlerefinementincryoelectrontomography AT irinagutsche flexibleframeworkformultiparticlerefinementincryoelectrontomography
_version_	1718375927955587072

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

Ejemplares similares