Protruding knob-like proteins violate local symmetries in an icosahedral marine virus

Nat Commun. 2014 Jul 2:5:4278. doi: 10.1038/ncomms5278.


Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Capsid / ultrastructure*
  • Capsid Proteins / chemistry*
  • Molecular Sequence Data
  • Podoviridae / ultrastructure*
  • Protein Conformation
  • Synechococcus / virology*


  • Capsid Proteins

Associated data

  • PDB/4BMI