Using cryoEM Reconstruction and Phase Extension to Determine
Crystal Structure of Bacteriophage I center dot 6 Major Capsid
Protein

J 2013

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein

NĚMEČEK, Daniel, Pavel PLEVKA and Evzen BOURA

Basic information

Original name

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein

Authors

NĚMEČEK, Daniel (203 Czech Republic, guarantor, belonging to the institution), Pavel PLEVKA (203 Czech Republic, belonging to the institution) and Evzen BOURA (203 Czech Republic)

Edition

The Protein Journal, NEW YORK, SPRINGER, 2013, 1572-3887

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 1.039

RIV identification code

RIV/00216224:14740/13:00072307

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1007/s10930-013-9526-x

UT WoS

000328080300006

Keywords in English

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

Abstract

V originále

Bacteriophage I center dot 6 is a double-stranded RNA virus that has been extensively studied as a model organism. Here we describe structure determination of I center dot 6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C222(1). 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 I center dot 6 procapsid at 7 resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. The averaged 3.6 -resolution electron density map was of sufficient quality to allow model building.

Citovat

NĚMEČEK, Daniel, Pavel PLEVKA and Evzen BOURA. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein. The Protein Journal. NEW YORK: SPRINGER, 2013, vol. 32, No 8, p. 635-640. ISSN 1572-3887. Available from: https://dx.doi.org/10.1007/s10930-013-9526-x.

@article{1166879,
   author = {Němeček, Daniel and Plevka, Pavel and Boura, Evzen},
   article_location = {NEW YORK},
   article_number = {8},
   doi = {http://dx.doi.org/10.1007/s10930-013-9526-x},
   keywords = {Molecular replacement; Cryo-electron microscopy; Non-crystallographic symmetry; Virus capsid protein; Phase extension},
   language = {eng},
   issn = {1572-3887},
   journal = {The Protein Journal},
   title = {Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein},
   url = {http://link.springer.com/article/10.1007%2Fs10930-013-9526-x},
   volume = {32},
   year = {2013}
}

TY  - JOUR
ID  - 1166879
AU  - Němeček, Daniel - Plevka, Pavel - Boura, Evzen
PY  - 2013
TI  - Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein
JF  - The Protein Journal
VL  - 32
IS  - 8
SP  - 635-640
EP  - 635-640
PB  - SPRINGER
SN  - 15723887
KW  - Molecular replacement
KW  - Cryo-electron microscopy
KW  - Non-crystallographic symmetry
KW  - Virus capsid protein
KW  - Phase extension
UR  - http://link.springer.com/article/10.1007%2Fs10930-013-9526-x
L2  - http://link.springer.com/article/10.1007%2Fs10930-013-9526-x
N2  - Bacteriophage I center dot 6 is a double-stranded RNA virus that has been extensively studied as a model organism. Here we describe structure determination of I center dot 6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C222(1). 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 I center dot 6 procapsid at 7 resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. The averaged 3.6 -resolution electron density map was of sufficient quality to allow model building.
ER  -

NĚMEČEK, Daniel, Pavel PLEVKA and Evzen BOURA. Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage I center dot 6 Major Capsid Protein. \textit{The Protein Journal}. NEW YORK: SPRINGER, 2013, vol.~32, No~8, p.~635-640. ISSN~1572-3887. Available from: https://dx.doi.org/10.1007/s10930-013-9526-x.

Detailed Information on Publication Record