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Bacteriophage PRD1 Capsid Structure: Iterative Combination of Threedimensional Electron Microscopy and X-Ray Crystallography

Published online by Cambridge University Press:  02 July 2020

Carmen San Martin ,
Roger M. Burnett ,
Felix de Haas ,
Ralph Heinkel ,
Twan Rutten ,
Stephen D. Fuller ,
Sarah J. Butcher  and
Dennis H. Bamford
Carmen San Martin
Affiliation:
The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania19104
Roger M. Burnett
Affiliation:
The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania19104
Felix de Haas
Affiliation:
Structural Biology Programme, EMBL, Meyerhofstraβe 1, Postfach 10.2209, 69117 Heidelberg, Germany
Ralph Heinkel
Affiliation:
Structural Biology Programme, EMBL, Meyerhofstraβe 1, Postfach 10.2209, 69117 Heidelberg, Germany
Twan Rutten
Affiliation:
Structural Biology Programme, EMBL, Meyerhofstraβe 1, Postfach 10.2209, 69117 Heidelberg, Germany
Stephen D. Fuller
Affiliation:
Structural Biology Programme, EMBL, Meyerhofstraβe 1, Postfach 10.2209, 69117 Heidelberg, Germany
Sarah J. Butcher
Affiliation:
Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
Dennis H. Bamford
Affiliation:
Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
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Extract

PRD1 is a ds-DNA bacteriophage from the Tectiviridae family with an unusual structural feature: the viral genome is enclosed by a protein-rich membrane, which is in turn enclosed by an external icosahedral protein shell (capsid). Three-dimensional reconstructions from cryo-electron microscopy (cryo-EM) images have revealed the structure of the PRD1 capsid at moderate resolution (28 Å), while X-ray crystallographic studies have recently provided a high resolution (1.85 Å) picture of the major coat protein, P3. We have now combined these results from different imaging methods to obtain a more detailed understanding of the virion organization. The combination has been made in a cyclic process: a preliminary fitting of the atomic structure of P3 to each one of its independent positions in the cryo-EM maps of the capsids provided initial models that could be used to improve the reconstructions; the refined maps then served as a base frame for an optimized fit. This process allows us to study the viral particle structure at “quasi-atomic” resolution.

Type
Electron Cryomicroscopy of Macromolecules
Information
Microscopy and Microanalysis , Volume 6 , Issue S2: Proceedings: Microscopy & Microanalysis 2000, Microscopy Society of America 58th Annual Meeting, Microbeam Analysis Society 34th Annual Meeting, Microscopical Society of Canada/Societe de Microscopie de Canada 27th Annual Meeting, Philadelphia, Pennsylvania August 13-17, 2000 , August 2000 , pp. 284 - 285
Copyright
Copyright © Microscopy Society of America

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References

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7. The authors wish to thank Janne Ravantti and Teemu Kivioja for providing programs used in this work, Marja-Leena Perala for technical assistance, and Stacy D. Benson for help in interpreting the P3 trimer atomic structure. CSM is a recipient of a Human Frontiers Science Program Postdoctoral Fellowship.Google Scholar