3J26

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of Sputnik, a virophage, at 3.5-A resolution.

Zhang, X.Sun, S.Xiang, Y.Wong, J.Klose, T.Raoult, D.Rossmann, M.G.

(2012) Proc.Natl.Acad.Sci.USA 109: 18431-18436

  • DOI: 10.1073/pnas.1211702109

  • 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 iden ...

    "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.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
capsid protein V20
A, B, C, D, E, F, G, H, I, J, K, L, M
508Sputnik virophageMutation(s): 0 
Find proteins for B4YNG0 (Sputnik virophage)
Go to UniProtKB:  B4YNG0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Minor virion protein
N
378Sputnik virophage 3Mutation(s): 0 
Find proteins for I0CES9 (Sputnik virophage 3)
Go to UniProtKB:  I0CES9
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-09-18 
  • Released Date: 2012-10-24 
  • Deposition Author(s): Zhang, X.Z.

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2012-11-14
    Type: Database references
  • Version 1.3: 2013-07-17
    Type: Other
  • Version 1.4: 2018-07-18
    Type: Data collection