Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling
High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidr...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2014
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| Online Access: | http://hdl.handle.net/1721.1/88254 https://orcid.org/0000-0001-6174-217X |
| _version_ | 1811076905131048960 |
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| author | Baker, Matthew L. Hryc, Corey F. Zhang, Qinfen Wu, Weimin Jakana, Joanita Haase-Pettingell, Cameron Afonine, Pavel V. Adams, Paul D. King, Jonathan Alan Jiang, Wen Chiu, Wah |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Baker, Matthew L. Hryc, Corey F. Zhang, Qinfen Wu, Weimin Jakana, Joanita Haase-Pettingell, Cameron Afonine, Pavel V. Adams, Paul D. King, Jonathan Alan Jiang, Wen Chiu, Wah |
| author_sort | Baker, Matthew L. |
| collection | MIT |
| description | High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages |
| first_indexed | 2024-09-23T10:30:16Z |
| format | Article |
| id | mit-1721.1/88254 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:30:16Z |
| publishDate | 2014 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/882542022-09-30T21:31:15Z Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling Baker, Matthew L. Hryc, Corey F. Zhang, Qinfen Wu, Weimin Jakana, Joanita Haase-Pettingell, Cameron Afonine, Pavel V. Adams, Paul D. King, Jonathan Alan Jiang, Wen Chiu, Wah Massachusetts Institute of Technology. Department of Biology Haase-Pettingell, Cameron King, Jonathan Alan High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages National Institutes of Health (U.S.) (Grant R01GM079429) National Institutes of Health (U.S.) (Grant P41GM103832) National Institutes of Health (U.S.) (Grant PN2EY016525) National Institutes of Health (U.S.) (Grant R56AI075208) Robert A. Welch Foundation (Q1242) National Institutes of Health (U.S.) (Grant GM063210) United States. Dept. of Energy (Contract DEAC0205CH11231) 2014-07-10T20:19:04Z 2014-07-10T20:19:04Z 2013-07 2013-04 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/88254 Baker, M. L., C. F. Hryc, Q. Zhang, W. Wu, J. Jakana, C. Haase-Pettingell, P. V. Afonine, et al. “Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling.” Proceedings of the National Academy of Sciences 110, no. 30 (July 23, 2013): 12301–12306. https://orcid.org/0000-0001-6174-217X en_US http://dx.doi.org/10.1073/pnas.1309947110 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Baker, Matthew L. Hryc, Corey F. Zhang, Qinfen Wu, Weimin Jakana, Joanita Haase-Pettingell, Cameron Afonine, Pavel V. Adams, Paul D. King, Jonathan Alan Jiang, Wen Chiu, Wah Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title | Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title_full | Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title_fullStr | Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title_full_unstemmed | Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title_short | Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling |
| title_sort | validated near atomic resolution structure of bacteriophage epsilon15 derived from cryo em and modeling |
| url | http://hdl.handle.net/1721.1/88254 https://orcid.org/0000-0001-6174-217X |
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