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Title: Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\Phi}$$6 Major Capsid Protein

Abstract

Bacteriophage $${\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\Phi}$$6 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 $${\Phi}$$6 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. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.

Authors:
 [1];  [1];  [2]
  1. Masaryk Univ., Brno (Czech Republic)
  2. Czech Academy of Sciences, Prague (Czech Republic). Inst. of Organic Chemistry and Biochemistry
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
MarieCurie; Academy of Sciences Czech Republic; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1314266
DOE Contract Number:  
W-31-109-Eng-38; FP7-PEOPLE-2012-CIG
Resource Type:
Journal Article
Resource Relation:
Journal Name: The Protein Journal; Journal Volume: 32; Journal Issue: 8
Country of Publication:
United States
Language:
ENGLISH
Subject:
Phase extension; Molecular; Cryo-electron microscopy; Non-crystallographic symmetry

Citation Formats

Nemecek, Daniel, Plevka, Pavel, and Boura, Evzen. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\Phi}$6 Major Capsid Protein. United States: N. p., 2013. Web. doi:10.1007/s10930-013-9526-x.
Nemecek, Daniel, Plevka, Pavel, & Boura, Evzen. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\Phi}$6 Major Capsid Protein. United States. doi:10.1007/s10930-013-9526-x.
Nemecek, Daniel, Plevka, Pavel, and Boura, Evzen. Fri . "Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\Phi}$6 Major Capsid Protein". United States. doi:10.1007/s10930-013-9526-x.
@article{osti_1314266,
title = {Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage ${\Phi}$6 Major Capsid Protein},
author = {Nemecek, Daniel and Plevka, Pavel and Boura, Evzen},
abstractNote = {Bacteriophage ${\Phi}$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of ${\Phi}$6 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 ${\Phi}$6 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. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.},
doi = {10.1007/s10930-013-9526-x},
journal = {The Protein Journal},
number = 8,
volume = 32,
place = {United States},
year = {Fri Nov 29 00:00:00 EST 2013},
month = {Fri Nov 29 00:00:00 EST 2013}
}