Scipion web tools: Easy to use cryo‐EM image processing over the web

Mingo, Pablo Conesa; Gutiérrez, J.A.; Quintana, Adrián; Trevín, José Miguel de la Rosa; Zaldívar-Peraza, A.; Alba, Jesús Cuenca; Kazemi, Mohsen; Vargas, Javier; Caño, Laura del; Segura, Joan; Sorzano, Carlos Óscar S.; Carazo, José Marı́a

doi:10.1002/pro.3315

Cited by 20 publications

(6 citation statements)

References 21 publications

(23 reference statements)

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“…The particles were then expanded according to I3 symmetry using RELION’s relion_particle_symmetry_expand function to obtain 60 times the 53,000 particles. A cylindrical mask ( r = 200 Å) was generated using Scipion 3.0 ( 67 ) and then resampled onto a reference map covering the fivefold vertex in UCSF Chimera ( 68 ). The cylindrical mask was then used for nonsampling 3D classification without imposing symmetry to search for the tail.…”

Section: Methodsmentioning

confidence: 99%

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Hou

Yang

et al. 2022

Sci. Adv.

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Sf6 is a bacterial virus that infects the human pathogen Shigella flexneri. Here, we describe the cryo–electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.

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Section: Methodsmentioning

confidence: 99%

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Hou

Yang

et al. 2022

Sci. Adv.

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“…cis TEM’s GUI required extensive development because it is an integral part of the processing pipeline. GUIs have become more commonplace in cryo-EM software tools to make them more accessible to users ( Conesa Mingo et al, 2018 ; Desfosses et al, 2014 ; Moriya et al, 2017 ; Punjani et al, 2017 ; Scheres, 2012 ; Tang et al, 2007 ). Many of the interfaces are designed as so-called wrappers of command-line driven tools, i.e.…”

Section: Resultsmentioning

confidence: 99%

cisTEM, user-friendly software for single-particle image processing

Grant

Rohou

Grigorieff

2018

eLife

854

542

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We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.

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“…The particles were then expanded according to I4 symmetry using RELION's relion_particle_symmetry_expand function to obtain 60 times the initial particles. A cylindrical mask (r = 200 Å) was generated using SCIPION 3.0 54 and then resampled onto a reference map covering the vefold vertex in Chimera 55 . The cylindrical mask was then used for non-sampling 3D classi cation without imposing symmetry to search for the tail.…”

Section: Cryo-em Spamentioning

confidence: 99%

Cryo-EM analysis of Pseudomonas phage Pa193 structural components

Cingolani,

Iglesias,

Hou

et al. 2024

Preprint

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The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.

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Scipion web tools: Easy to use cryo‐EM image processing over the web

Cited by 20 publications

References 21 publications

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

cisTEM, user-friendly software for single-particle image processing

Cryo-EM analysis of Pseudomonas phage Pa193 structural components

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