Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 840-mer - A780B60 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 773.90 kDa 
• Atom Count: 54479 
• Modelled Residue Count: 6966 
• Deposited Residue Count: 6982 
• Unique protein chains: 2

3J26

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

• PDB DOI: 10.2210/pdb3J26/pdb
• EM Map EMD-5495: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Sputnik virophage
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 U S A 109: 18431-18436

• PubMed: 23091035 
• DOI: 10.1073/pnas.1211702109
• Primary Citation of Related Structures:  
  3J26


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein V20	A, B, C, D, E, F, G, H, I, J, K, L, M	508	Sputnik virophage	Mutation(s): 0  Gene Names: ORF20
UniProt
Find proteins for B4YNG0 (Sputnik virophage) Explore B4YNG0  Go to UniProtKB:  B4YNG0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor virion protein	N	378	Sputnik virophage	Mutation(s): 0
UniProt
Find proteins for I0CES9 (Sputnik virophage 3) Explore I0CES9  Go to UniProtKB:  I0CES9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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
  Changes: Database references
• Version 1.2: 2012-11-14
  Changes: Database references
• Version 1.3: 2013-07-17
  Changes: Other
• Version 1.4: 2018-07-18
  Changes: Data collection