3J40

Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling

Replaces:  3C5B

Summary for 3J40

• Entry DOI: 10.2210/pdb3j40/pdb
• EMDB information: 5678
• Descriptor: gp10, gp7 (2 entities in total)
• Functional Keywords: capsid, accessory protein, virus
• Biological source: Salmonella phage epsilon15; More
• Total number of polymer chains: 14
• Total formula weight: 343265.22

Authors

Baker, M.L.,Hryc, C.F.,Zhang, Q.,Wu, W.,Jakana, J.,Haase-Pettingell, C.,Afonine, P.V.,Adams, P.D.,King, J.A.,Jiang, W.,Chiu, W. (deposition date: 2013-05-30, release date: 2013-07-10, Last modification date: 2024-02-21)

Primary citation

Baker, M.L.,Hryc, C.F.,Zhang, Q.,Wu, W.,Jakana, J.,Haase-Pettingell, C.,Afonine, P.V.,Adams, P.D.,King, J.A.,Jiang, W.,Chiu, W.
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.
Proc.Natl.Acad.Sci.USA, 110:12301-12306, 2013

PubMed 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.

PubMed: 23840063
DOI: 10.1073/pnas.1309947110

Experimental method

ELECTRON MICROSCOPY (4.5 Å)