3J26

The 3.5 A resolution structure of the Sputnik virophage by cryo-EM

Summary for 3J26

• Entry DOI: 10.2210/pdb3j26/pdb
• EMDB information: 5495
• Descriptor: capsid protein V20, Minor virion protein (2 entities in total)
• Functional Keywords: double jelly-roll, single jelly-roll, virus
• Biological source: Sputnik virophage; More
• Total number of polymer chains: 14
• Total formula weight: 773897.04

Authors

Zhang, X.Z. (deposition date: 2012-09-18, release date: 2012-10-24, Last modification date: 2024-02-21)

Primary citation

Zhang, X.,Sun, S.,Xiang, Y.,Wong, J.,Klose, T.,Raoult, D.,Rossmann, M.G.
Structure of Sputnik, a virophage, at 3.5-A resolution.
Proc.Natl.Acad.Sci.USA, 109:18431-18436, 2012

PubMed Abstract: "Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.

PubMed: 23091035
DOI: 10.1073/pnas.1211702109

Experimental method

ELECTRON MICROSCOPY (3.5 Å)