The Protein Journal

, Volume 32, Issue 8, pp 635–640 | Cite as

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ϕ6 Major Capsid Protein

  • Daniel Nemecek
  • Pavel Plevka
  • Evzen Boura


Bacteriophage ϕ6 is a double-stranded RNA virus that has been extensively studied as a model organism. Here we describe structure determination of ϕ6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the ϕ6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. The averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.


Molecular replacement Cryo-electron microscopy Non-crystallographic symmetry Virus capsid protein Phase extension 



Non-crystallographic symmetry


Cryo-electron microscopy



This research was supported by MarieCurie FP7-PEOPLE-2012-CIG, project number 333916, and by Academy of Sciences Czech Republic (RVO: 61388963). Crystallographic data were collected at the Southeast Regional Collaborative Access Team 22-ID beamline at the Advanced Photon Source, Argonne National Laboratory. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under contract W-31-109-Eng-38.


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
  2. 2.Institute of Organic Chemistry and Biochemistry AS CRPrague 6Czech Republic

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