Applying 3D ED/MicroED workflows toward the next frontiers
Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic
Typ dokumentu časopisecké články
Grantová podpora
2132227
National Science Foundation
956099
EU H2020 ITN project NanED
5R01GM141273
National Institutes of Health, National Institute of General Medical Sciences
SF349247
Simons Foundation
P30 CA008748
NCI NIH HHS - United States
R01 GM141273
NIGMS NIH HHS - United States
BB/S007040/1
Biotechnology and Biological Sciences Research Council - United Kingdom
P30GM103546
National Institutes of Health, National Institute of General Medical Sciences
U24 GM129539
NIGMS NIH HHS - United States
P20 GM103546
NIGMS NIH HHS - United States
PubMed
38712546
PubMed Central
PMC11150879
DOI
10.1107/s2053229624004078
PII: S2053229624004078
Knihovny.cz E-zdroje
- Klíčová slova
- 3D ED, MicroED, electron diffraction, microcrystal electron diffraction,
- MeSH
- elektronová kryomikroskopie * MeSH
- průběh práce MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.
Chemistry and Biochemistry University of Montana 32 Campus Drive Missoula Montana 59812 USA
Department of Cell Biology NYU Grossman School of Medicine 540 1st Ave New York New York 10016 USA
Department of Chemistry Princeton University Princeton New Jersey 08544 USA
Department of Chemistry Yale University New Haven Connecticut 06520 USA
Gatan Inc Pleasanton CA 94588 USA
Hauptman Woodward Medical Research Institute 700 Ellicott St Buffalo New York 14203 USA
Institute of Physics of the CAS NanED Na Slovance 1999 2 Prague 192000 Czech Republic
Materials Research Laboratory University of Illinois at Urbana Champaign Urbana Illinois 61801 USA
Memorial Sloan Kettering Cancer Center 1275 York Avenue New York New York 10065 USA
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Alexander, B. W., Bartfield, N. M., Gupta, V., Mercado, B. Q., Del Campo, M. & Herzon, S. B. (2024). Science, 383, 849–854. PubMed
Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. (2011). Acta Cryst. D67, 271–281. PubMed PMC
Brázda, P., Palatinus, L. & Babor, M. (2019). Science, 364, 667–669. PubMed
Broadhurst, E. T., Xu, H., Parsons, S. & Nudelman, F. (2021). IUCrJ, 8, 860–866. PubMed PMC
Bruhn, J. F., Scapin, G., Cheng, A., Mercado, B. Q., Waterman, D. G., Ganesh, T., Dallakyan, S., Read, B. N., Nieusma, T., Lucier, K. W., Mayer, M. L., Chiang, N. J., Poweleit, N., McGilvray, P. T., Wilson, T. S., Mashore, M., Hennessy, C., Thomson, S., Wang, B., Potter, C. S. & Carragher, B. (2021). Front. Mol. Biosci. 8, 648603. PubMed PMC
Cheng, A., Negro, C., Bruhn, J. F., Rice, W. J., Dallakyan, S., Eng, E. T., Waterman, D. G., Potter, C. S. & Carragher, B. (2021). Protein Sci. 30, 136–150. PubMed PMC
Clabbers, M. T. B., Gruene, T., Parkhurst, J. M., Abrahams, J. P. & Waterman, D. G. (2018). Acta Cryst. D74, 506–518. PubMed PMC
Clabbers, M. T. B., Martynowycz, M. W., Hattne, J., Nannenga, B. L. & Gonen, T. (2022). J. Struct. Biol. 214, 107886. PubMed PMC
Cruz, M. J. de la (2021). cryoEM: Methods and Protocols, edited by T. Gonen & B. L. Nannenga, Methods in Molecular Biology, Vol. 2215, pp. 321–327. Totowa, New Jersey: Humana.
Cruz, M. J. de la & Eng, E. T. (2023). Structure, 31, 1487–1498. PubMed PMC
Cruz, M. J. de la, Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F. E., Sawaya, M. R., Cascio, D., Weiss, S. C., Kim, S. K., Hinck, C. S., Hinck, A. P., Calero, G., Eisenberg, D. & Gonen, T. (2017). Nat. Methods, 14, 399–402. PubMed PMC
Dandey, V. P., Wei, H., Zhang, Z., Tan, Y. Z., Acharya, P., Eng, E. T., Rice, W. J., Kahn, P. A., Potter, C. S. & Carragher, B. (2018). J. Struct. Biol. 202, 161–169. PubMed PMC
Danelius, E., Bu, G., Wieske, L. H. E. & Gonen, T. (2023). ACS Chem. Biol. 18, 2582–2589. PubMed PMC
Delgadillo, D. A., Burch, J. E., Kim, L. J., de Moraes, L. S., Niwa, K., Williams, J., Tang, M. J., Lavallo, V. G., Khatri Chhetri, B., Jones, C. G., Rodriguez, I. H., Signore, J. A., Marquez, L., Bhanushali, R., Woo, S., Kubanek, J., Quave, C., Tang, Y. & Nelson, H. M. (2024). ACS Cent. Sci. 10, 176–183. PubMed PMC
Duyvesteyn, H. M. E., Kotecha, A., Ginn, H. M., Hecksel, C. W., Beale, E. V., de Haas, F., Evans, G., Zhang, P., Chiu, W. & Stuart, D. I. (2018). Proc. Natl Acad. Sci. USA, 115, 9569–9573. PubMed PMC
Ge, M., Wang, Y., Carraro, F., Liang, W., Roostaeinia, M., Siahrostami, S., Proserpio, D. M., Doonan, C., Falcaro, P., Zheng, H., Zou, X. & Huang, Z. (2021). Angew. Chem. Int. Ed. 60, 11391–11397. PubMed PMC
Ge, M., Yang, T., Xu, H., Zou, X. & Huang, Z. (2022). J. Am. Chem. Soc. 144, 15165–15174. PubMed PMC
Gemmi, M., Mugnaioli, E., Gorelik, T. E., Kolb, U., Palatinus, L., Boullay, P., Hovmöller, S. & Abrahams, J. P. (2019). ACS Cent. Sci. 5, 1315–1329. PubMed PMC
Ghosh, R., Bu, G., Nannenga, B. L. & Sumner, L. W. (2021). Front. Mol. Biosci. 8, 720955. PubMed PMC
Gillman, C., Nicolas, W. J., Martynowycz, M. W. & Gonen, T. (2023). IUCrJ, 10, 430–436. PubMed PMC
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. PubMed PMC
Gruene, T., Wennmacher, J. T. C., Zaubitzer, C., Holstein, J. J., Heidler, J., Fecteau–Lefebvre, A., De Carlo, S., Müller, E., Goldie, K. N., Regeni, I., Li, T., Santiso–Quinones, G., Steinfeld, G., Handschin, S., van Genderen, E., van Bokhoven, J. A., Clever, G. H. & Pantelic, R. (2018). Angew. Chem. Int. Ed. 57, 16313–16317. PubMed PMC
Hadermann, J. & Abakumov, A. M. (2019). Acta Cryst. B75, 485–494. PubMed
Hadermann, J. & Palatinus, L. (2019). Acta Cryst. B75, 462. PubMed
Hattne, J., Clabbers, M. T. B., Martynowycz, M. W. & Gonen, T. (2023). Structure, 31, 1504–1509.e1. PubMed PMC
Hogan-Lamarre, P., Luo, Y., Bücker, R., Miller, R. J. D. & Zou, X. (2024). IUCrJ, 11, 62–72. PubMed PMC
Ito, S., White, F. J., Okunishi, E., Aoyama, Y., Yamano, A., Sato, H., Ferrara, J. D., Jasnowski, M. & Meyer, M. (2021). CrystEngComm, 23, 8622–8630.
Jones, C. G., Martynowycz, M. W., Hattne, J., Fulton, T. J., Stoltz, B. M., Rodriguez, J. A., Nelson, H. M. & Gonen, T. (2018). ACS Cent. Sci. 4, 1587–1592. PubMed PMC
Kabsch, W. (2010). Acta Cryst. D66, 125–132. PubMed PMC
Karothu, D. P., Alhaddad, Z., Göb, C. R., Schürmann, C. J., Bücker, R. & Naumov, P. (2023). Angew. Chem. Int. Ed. 62, e202303761. PubMed
Kim, L. J., Ohashi, M., Zhang, Z., Tan, D., Asay, M., Cascio, D., Rodriguez, J. A., Tang, Y. & Nelson, H. M. (2021). Nat. Chem. Biol. 17, 872–877. PubMed PMC
Kim, L. J., Xue, M., Li, X., Xu, Z., Paulson, E., Mercado, B., Nelson, H. M. & Herzon, S. B. (2021). J. Am. Chem. Soc. 143, 6578–6585. PubMed PMC
Kingwell, K. (2023). Nat. Rev. Drug Discov. 22, 771–773. PubMed
Klar, P. B., Krysiak, Y., Xu, H., Steciuk, G., Cho, J., Zou, X. & Palatinus, L. (2023). Nat. Chem. 15, 848–855. PubMed PMC
Klementová, M., Karlík, M., Novák, P. & Palatinus, L. (2017). Intermetallics, 85, 110–116.
Kolb, U., Gorelik, T. & Mugnaioli, E. (2009). MRS Proc. 1184, 1184-GG01-05.
Kolb, U., Gorelik, T. & Otten, M. T. (2008). Ultramicroscopy, 108, 763–772. PubMed
Kolb, U., Mugnaioli, E. & Gorelik, T. E. (2011). Cryst. Res. Technol. 46, 542–554.
Li, C., Ding, C., Li, M., Rong, J., Florian, H. & Simpson, G. (2021). Acta Cryst. D77, 463–470. PubMed PMC
Lin, J., Unge, J. & Gonen, T. (2023). Adv. Sci. 10, 202304476. PubMed PMC
Lin, J., Unge, J. & Gonen, T. (2024). Adv. Sci. 11, 202306435. PubMed PMC
Lynch, M. L., Snell, M. E., Potter, S. A., Snell, E. H. & Bowman, S. E. J. (2023). Acta Cryst. D79, 198–205. PubMed PMC
Martynowycz, M. W. & Gonen, T. (2021). STAR Protoc. 2, 100686. PubMed PMC
Martynowycz, M. W., Shiriaeva, A., Clabbers, M. T. B., Nicolas, W. J., Weaver, S. J., Hattne, J. & Gonen, T. (2023). Nat. Commun. 14, 1086. PubMed PMC
Martynowycz, M. W., Zhao, W., Hattne, J., Jensen, G. J. & Gonen, T. (2019). Structure, 27, 545–548. PubMed PMC
McPherson, A. & Gavira, J. A. (2014). Acta Cryst. F70, 2–20. PubMed PMC
Midgley, P. A. & Eggeman, A. S. (2015). IUCrJ, 2, 126–136. PubMed PMC
Miller, R. D., Iinishi, A., Modaresi, S. M., Yoo, B.-K., Curtis, T. D., Lariviere, P. J., Liang, L., Son, S., Nicolau, S., Bargabos, R., Morrissette, M., Gates, M. F., Pitt, N., Jakob, R. P., Rath, P., Maier, T., Malyutin, A. G., Kaiser, J. T., Niles, S., Karavas, B., Ghiglieri, M., Bowman, S. E. J., Rees, D. C., Hiller, S. & Lewis, K. (2022). Nat. Microbiol. 7, 1661–1672. PubMed PMC
Palatinus, L., Brázda, P., Jelínek, M., Hrdá, J., Steciuk, G. & Klementová, M. (2019). Acta Cryst. B75, 512–522. PubMed
Park, J., Li, Y., Moon, K., Han, E. J., Lee, S. R. & Seyedsayamdost, M. R. (2022). Angew. Chem. Int. Ed. 61, e202114022. PubMed PMC
Polovinkin, V., Khakurel, K., Babiak, M., Angelov, B., Schneider, B., Dohnalek, J., Andreasson, J. & Hajdu, J. (2020). J. Appl. Cryst. 53, 1416–1424. PubMed PMC
Pratim Das, P., Ponce-Pedraza, A., Mugnaioli, E. & Nicolopoulos, S. (2022). Symmetry, 14, https://www.mdpi.com/journal/symmetry/special_issues/Electron_Diffraction_Structural_Imaging_II.
Saha, A., Nia, S. S. & Rodríguez, J. A. (2022). Chem. Rev. 122, 13883–13914. PubMed PMC
Sasaki, T., Nakane, T., Kawamoto, A., Nishizawa, T. & Kurisu, G. (2023). CrystEngComm, 25, 352–356.
Shoeman, R. L., Hartmann, E. & Schlichting, I. (2023). Nat. Protoc. 18, 854–882. PubMed
Simoncic, P., Romeijn, E., Hovestreydt, E., Steinfeld, G., Santiso-Quiñones, G. & Merkelbach, J. (2023). Acta Cryst. E79, 410–422. PubMed PMC
Smeets, S., Wang, B. & Hogenbirk, E. (2021). https://zenodo.org/records/5175957.
Spek, A. L. (2020). Acta Cryst. E76, 1–11. PubMed PMC
Steciuk, G., David, A., Petříček, V., Palatinus, L., Mercey, B., Prellier, W., Pautrat, A. & Boullay, P. (2019). J. Appl. Cryst. 52, 626–636.
Unge, J., Lin, J., Weaver, S. J., Sae Her, A. & Gonen, T. (2023). ChemRxiv. https://doi.org/10.26434/chemrxiv-2023-8qvwg.
Vincent, R. & Midgley, P. A. (1994). Ultramicroscopy, 53, 271–282.
Wan, W., Sun, J., Su, J., Hovmöller, S. & Zou, X. (2013). J. Appl. Cryst. 46, 1863–1873. PubMed PMC
Wang, B., Zou, X. & Smeets, S. (2019). IUCrJ, 6, 854–867. PubMed PMC
Waterman, D. G., Frisina, N., Owen, C. D., Winter, G. & Nunes, P. (2023). Structure, 31, 1510–1517. PubMed
Weiss, S., Vergara, S., Lin, G. & Calero, G. (2021). cryoEM: Methods and Protocols, edited by T. Gonen & B. L. Nannenga, Methods in Molecular Biology, Vol. 2215, pp. 299–307. Totowa, New Jersey: Humana. PubMed PMC
Winter, G., Waterman, D. G., Parkhurst, J. M., Brewster, A. S., Gildea, R. J., Gerstel, M., Fuentes-Montero, L., Vollmar, M., Michels-Clark, T., Young, I. D., Sauter, N. K. & Evans, G. (2018). Acta Cryst. D74, 85–97. PubMed PMC
Yang, T., Willhammar, T., Xu, H., Zou, X. & Huang, Z. (2022). Nat. Protoc. 17, 2389–2413. PubMed
Yonekura, K., Ishikawa, T. & Maki-Yonekura, S. (2019). J. Struct. Biol. 206, 243–253. PubMed
Zhao, J., Xu, H., Lebrette, H., Carroni, M., Taberman, H., Högbom, M. & Zou, X. (2021). Nat. Commun. 12, 5036. PubMed PMC
Zhou, G., Yang, T. & Huang, Z. (2023). Commun. Chem. 6, 116. PubMed PMC