Structure determination of coxsackievirus B3 to 3.5 Å resolution

Abstract

The crystal structure of coxsackievirus B3 (CVB3) has been determined to 3.5,4, resolution. The icosahedral CVB3 panicles crystallize in the monoclinic space group, P21, (a--574.6, b = 302.1, c---521.6A, /3--107.7 °) with two virions in the asymmetric unit giving 120-fold non-crystallographic redundancy. The crystals diffracted to 2.7 A resolution and the X-ray data set was 55% complete to 3.0,4, resolution. Systematically weak reflections and the self-rotation function established pseudo R32 symmetry with each particle sitting on a 32 special position. This constrained the orientation and position of each panicle in the monoclinic cell to near face-centered positions and allowed for a total of six possible monoclinic spacegroup settings. Correct interpretation of the highresolution (3.0-3.2~,) self-rotation function was instrumental in determining the deviations from R32 orientations of the virus particles in the unit cell. Accurate particle orientations permitted the correct assignment of the crystal space-group setting amongst the six ambiguous possibilities and for the correct determination of particle positions. Real-space electron-density averaging and phase refinement, using human rhinovius 14 (HRV14) as an initial phasing model, have been carried out to 3.5,~ resolution. The initial structural model has been built and refined to 3.5 ~, resolution using X-PLOR.

Structural and Virological Studies of the Stages of Virus Replication That Are Affected by Antirhinovirus Compounds

“…This ligand is probably a lipid-like molecule derived from the host cell (10,21,33,34), although solvent molecules, such as polyethylene glycol used in crystallization (47), have also been found to bind. It has been hypothesized that pocket factor binding in this hydrophobic cavity plays a role in maintaining picornavirus capsid stability (24,34,41).…”

Molecular mechanism of a specific capsid binder resistance caused by mutations outside the binding pocket

“…Homology models for CVB3 97927 were manually derived from PDB structure 1COV (Muckelbauer et al, 1995b). Molecular dynamics simulations were carried out using the AMBER11 (with patches up to 17 applied) and the AMBERTOOLS version 1.5 suite of programs Homology models for the CVB3 97927 variants were derived using PDB 1cov (Muckelbauer et al, 1995b) as a template.…”

“…Molecular dynamics simulations were carried out using the AMBER11 (with patches up to 17 applied) and the AMBERTOOLS version 1.5 suite of programs Homology models for the CVB3 97927 variants were derived using PDB 1cov (Muckelbauer et al, 1995b) as a template. Molecular dynamics simulations were carried out using AMBER11 and the AMBERTOOLS suite of programs (Case et al, 2010) (Case et al, 2010).…”

“…Homology models for the CVB3 97927 variants were derived using PDB 1cov (Muckelbauer et al, 1995b) as a template. Molecular dynamics simulations were carried out using AMBER11 and the AMBERTOOLS suite of programs (Case et al, 2010).…”

Structure Determination of Echovirus 1

“…This problem was easy to correct, as only one other choice of primitive orthorhombic space group was consistent with the observed packing, pseudo-centering and particle rotation and was capable of resolving the problem with the h + l odd terms. Several of the virus crystal structures solved in recent years exhibit higher order pseudo-symmetries (Muckelbauer, Kremer, Minor, Tong et al, 1995;Zlotnick et al, 1997) suggesting that the use of pseudocentering to limit the size of the molecular-replacement problem could be applied generally.…”