Structure and assembly model for the
            <i>Trypanosoma cruzi</i>
            60S ribosomal subunit

Liu, Zheng; Gutierrez-Vargas, Cristina; Jia, Wei; Grassucci, Robert A.; Ramesh, Madhumitha; Espina, Noel; Sun, Ming; Tutuncuoglu, Beril; Madison‐Antenucci, Susan; Woolford, John L.; Tong, Liang; Frank, Joachim

doi:10.1073/pnas.1614594113

Cited by 68 publications

(83 citation statements)

References 45 publications

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“…The structure of the Trypanosoma cruzi 60S ribosomal subunit was determined at 2.54 Å resolution (PDB ID 5t5h (Liu et al, 2016b)). Only one map, presumably the sharpened one (EMD-8361), is present in both the PDB and EMDB.…”

Section: Resultsmentioning

confidence: 99%

High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective

Wlodawer

Dauter

2017

Structure

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Summary The appearance of ten high-resolution cryo-EM maps of proteins, ribosomes, and viruses was compared to the experimentally phased crystallographic electron density maps of four proteins. We found that maps calculated at a similar resolution by the two techniques are quite comparable in their appearance, although cryo-EM maps, even when sharpened, seem to be a little less detailed. An analysis of models fitted to the cryo-EM maps indicated the presence of significant problems in almost all of them, including incorrect geometry, clashes between atoms, and discrepancies between the map density and the fitted models. In particular, the treatment of the atomic displacement (B) factors was meaningless in almost all analyzed cryo-EM models. Stricter cryo-EM structure deposition standards and their better enforcement are needed.

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Section: Resultsmentioning

confidence: 99%

High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective

Wlodawer

Dauter

2017

Structure

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“…The most common mode is the use of FEI microscopes, in particular the Titan Krios, for high-resolution cryo-EM, RELION for image processing and the Gatan K2 camera for high-resolution work. However, other technological solutions have also been shown to give comparable results, for example a 3.4 Å resolution alcohol oxidase structure obtained using a Jeol 3200FSC microscope (Vonck et al, 2016), a 1.8 Å resolution glutamate dehydrogenase structure obtained using the FREALIGN software package (Merk et al, 2016) and a 2.5 Å resolution Trypanosoma cruzi 60S ribosomal subunit structure (Liu et al, 2016) obtained using a Falcon II camera. Furthermore, competitors are trying to redress the imbalance with new and improved solutions; for instance, Jeol with a new automatic specimen-loading system, a redesigned FREALIGN with a graphical user interface (cisTEM; personal communication with Timothy Grant, Janelia Research Campus), and the FEI Falcon III camera, which will even be retrofitted onto the most recently sold FEI microscope systems with a Falcon II camera.…”

Section: Discussionmentioning

confidence: 95%

Trends in the Electron Microscopy Data Bank (EMDB)

Patwardhan

2017

Acta Crystallogr D Struct Biol

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Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.

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“…Even though Ih ave illustrated the progress achieved by using my favorite molecule,t he ribosome (best resolution thus far at 2.5 ; [93] Figure 24 a), the range of applications in biology is virtually unlimited except for some lower bound on molecule size,a nd, of course,t he necessity of having the molecule suspended in solution. My own recent collabora- Figure 22.…”

Section: Move To Columbia University-story In Asamplementioning

confidence: 99%