Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Sorzano, C.O.S.; Semchonok, Dmitry A.; Lin, Su Chang; Lo, Yi-Ching; Vilas, José Luis; Jiménez-Moreno, Amaya; Gragera, Marcos; Vacca, Santiago; Maluenda, David; Martínez, Marta; Ramírez-Aportela, Erney; Melero, R.; Cuervo, Ana; Conesa, José Javier; Conesa, Pablo; Losana, Patricia; Caño, Laura del; Morena, J. Jiménez de la; Fonseca, Yunior C.; Sánchez-García, Rubén J.; Střelák, David; Fernández-Giménez, E.; Isidro, Federico De; Herreros, David; Kastritis, Panagiotis L.; Marabini, Roberto; Bruce, Barry D.; Carazo, José Marı́a

doi:10.1016/j.jsb.2020.107695

Cited by 26 publications

(23 citation statements)

References 28 publications

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“…The 3D classification was performed using the RELION 3.0 3D classification protocol ( Scheres, 2016 ). The best 3D class outcome 122 411 particles were subjected to further refinement protocol using Xmipp highres ( de la Rosa-Trevin et al., 2016 ; Sorzano et al., 2018 , 2021 ). The resulting refined cryo-EM 3D map contained 66 130 particles.…”

Section: Methodsmentioning

confidence: 99%

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Semchonok

Mondal

Cooper

et al. 2022

Plant Communications

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Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI of cyanobacteria exists in monomeric, trimeric, and tetrameric forms, in contrast to the strictly monomeric form of PSI in plants and algae. The tetrameric organization raises questions about its structural, physiological, and evolutionary significance. Here we report the ∼3.72 Å resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. The structure resolves 44 subunits and 448 cofactor molecules. We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization. The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers. Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state. Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

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Section: Methodsmentioning

confidence: 99%

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Semchonok

Mondal

Cooper

et al. 2022

Plant Communications

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“…In [64], we suggested that principal component analysis (PCA) is a useful tool to analyze flexibility, but only at low resolution. In [65], we analyzed the sensitivity to preferred orientations of several image processing algorithms used for angular assignment and 3D reconstruction. Then, we showed how to combine Xmipp and other plugins in Scipion to distinguish correctly from incorrectly estimated parameters of the processing pipeline to achieve a more confident assessment about the reconstructed structures [66].…”

Section: Our Other Contributions and Xmipp Applicationsmentioning

confidence: 99%

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

et al. 2021

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Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

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“…By optimising the wait time between sample loading and blotting, we improved the distribution of the side view by approximately 10% (figure 2a 3 ). The preferential orientation issue is biological specimen dependent, and many options may proceed case by case (Han et al, 2020, Sorzano et al, 2021, Tan et al, 2017. If the particles are two linked PSI tetramer, then the preferential orientation is relatively inevitable as the hydrophilic area of top view is as large as around 1000 nm 2 , while it is less than 200 nm 2 in side view (supplementary figure 1).…”

Section: Cryo-em Structure Of Psi Octamer Complexmentioning

confidence: 99%

Structure Insight into Photosystem I Octamer from Cyanobacteria

Chen

Liu

et al. 2021

Preprint

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Diversity of photosystem oligomers is essential to understand how photosynthetic organisms adopted to light conditions. Given by the structural and physiological significance, the assemblies of PSI supercomplex is of great interest in both chloroplast and cyanobacteria recently. In this study, two novel photosystem I supercomplexes were isolated for the first time from the low light incubated culture of filamentous cyanobacterium Anabaena sp. PCC 7120. These complexes were defined as PSI hexamers and octamers through biochemical and biophysical characterization. Their 77K emission spectra indicated that the red forms of chlorophylls seemed not to be affected during oligomerization. By cryo-EM single particle analysis, a near-atomic (7.0 Å) resolution structure of PSI octamer was resolved, and the molecular assemblies of stable PSI octamer was revealed.

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Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Cited by 26 publications

References 28 publications

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

Structure Insight into Photosystem I Octamer from Cyanobacteria

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