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Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12301-6. doi: 10.1073/pnas.1309947110. Epub 2013 Jul 9.

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.

Author information

1
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

Abstract

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.

KEYWORDS:

EMAN; PHENIX; Pathwalker; gold standard; validation

PMID:
23840063
PMCID:
PMC3725109
DOI:
10.1073/pnas.1309947110
[Indexed for MEDLINE]
Free PMC Article
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