A monoclinic crystal with R32 pseudo-symmetry: a preliminary report of Nodamura virus structure determination

Zlotnick, Adam; McKinney, B. R.; Munshi, Sanjeev; Bibler, J.K.; Rossmann, Michael G.; Johnson, John E.

doi:10.1107/s0907444993007498

Cited by 5 publications

(10 citation statements)

References 3 publications

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“…As an icosahedral twofold axes of each of the two icosahedral particles in the asymmetric unit was nearly parallel to the monoclinic twofold axis, it might have been expected that the positions of the particles could have been determined by looking for Harker peaks between symmetry-related particles (Tsao et al, 1992;Zlotnick et al, 1993). However, such peaks were hidden behind diffraction ripples around the 'origin peaks' caused by the pseudo face-centered symmetry.…”

Section: Patterson Analysismentioning

confidence: 99%

“…Nodamura virus (NOV) also exhibited pseudo R32 symmetry and packed similarly to CVB3 in a monoclinic P2~ cell with two particles in the asymmetric unit (Zlotnick et al, 1993).While the cell dimensions and the P2 L space group were similar for CVB3 and NOV, the pseudo R32 symmetry for NOV was much less severe than that of CVB3. The less extensive pseudo symmetry was most evident based on the presence of the systematically weak pseduo R32 reflections at low resolution, the obvious splitting of the self-rotation function peaks at 3.5,4, resolution and the displacements of the particles from the special face-centered positions.…”

Section: Introductionmentioning

confidence: 99%

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Structure determination of coxsackievirus B3 to 3.5 Å resolution

Muckelbauer

Kremer²,

Minor³

et al. 1995

Acta Crystallogr D Biol Crystallogr

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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.

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Section: Patterson Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structure determination of coxsackievirus B3 to 3.5 Å resolution

Muckelbauer

Kremer²,

Minor³

et al. 1995

Acta Crystallogr D Biol Crystallogr

Self Cite

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“…Self-rotation functions, computed with reflections in the resolution range 3.9-3.7 A from the partial data set reported by Zlotnick et al (1993) yielded a constellation of peaks consistent with the orientation of a single icosahedron for the four particles in the unit cell. This showed that the particles were in nearly identical orientations with an icosahedral twofold axis of the independent particles in the asymmetric unit being nearly parallel to the crystallographic twofold axis (b axis).…”

Section: Rotation-function Solutionmentioning

confidence: 87%

“…Preparation of material, crystallization and a preliminary analysis of a partial data set collected on film have been reported by Zlotnick et al (1993). Table 1 …”

Section: Data Collection and Processingmentioning

confidence: 99%

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Resolution of Space-Group Ambiguity and Structure Determination of Nodamura Virus to 3.3 Å resolution from Pseudo-R32 (Monoclinic) Crystals

Zlotnick¹,

Natarajan²,

Munshi³

et al. 1997

Acta Crystallogr D Biol Crystallogr

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Monoclinic crystals of nodamura virus (NOV) have two virus molecules per asymmetric unit. Packing analysis reveals a pseudo-rhombohedral (pseudo-C2 monoclinic) arrangement of particles in the actual P21 space group (a = 562.1, b = 354.1, c = 612.8 ]k,/3 = 110.9'~). The R32 symmetry is broken rotationally and translationally. The pseudo-symmetry of the unit cell results in three possible monoclinic origins and also restrains the four particles in the unit cell to similar orientations. NOV particles deviate by less than 3 from the ideal orientations, causing overlap of peaks in the rotation function and the generation of peaks that were not interpretable as particle symmetry elements. The space-group ambiguity was resolved by analysing the relationship between the particle orientations determined by high-resolution rotation functions and the attenuation of peak heights in native Patterson maps. Particles were centered less than 1A from the R32 special positions. Three different approaches were required to identify the correct particle center. Following the solutions of the rotation and translation problems, phases were computed using the coordinates of flock house virus (FHV), another member of this virus family. The phases were improved by realspace molecular averaging with a 120-fold non-crystallographic symmetry and by solvent flattening with a spherical mask. The final model for the NOV structure was built using the 3.3 A averaged map. While the overall subunit structure was very similar to that of other nodaviruses, FHV and black beetle virus, NOV showed distinct structural features near particle threefold and quasi-threefold axes and at the protein-RNA interfaces that are consistent with phenotype differences among the related viruses.

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The extracellular domain of immunodeficiency virus gp41 protein: Expression inEscherichia coli, purification, and crystallization

et al. 1997

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The env gene of SIV and HIV-I encodes a single glycoprotein gp160, which is processed to give a noncovalent complex of the soluble glycoprotein gp120 and the transmembrane glycoprotein gp41. The extracellular region (ectodomain), minus the N-terminal fusion peptide, of gp41 from HIV-1 (residues 27-154) and SIV (residues 27-149) have been expressed in Escherichia coli. These insoluble proteins were solubilized and subjected to a simple purification and folding scheme, which results in high yields of soluble protein. Purified proteins have a trimeric subunit composition and high a-helical content, consistent with the predicted coil-coil structure. SIV gp41 containing a double cysteine mutation was crystallized. The crystals are suitable for X-ray structure determination and, preliminary analysis, together with additional biochemical evidence, indicates that the gp41 trimer is arranged as a parallel bundle with threefold symmetry.

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A monoclinic crystal with R32 pseudo-symmetry: a preliminary report of Nodamura virus structure determination

Cited by 5 publications

References 3 publications

Structure determination of coxsackievirus B3 to 3.5 Å resolution

Structure determination of coxsackievirus B3 to 3.5 Å resolution

Resolution of Space-Group Ambiguity and Structure Determination of Nodamura Virus to 3.3 Å resolution from Pseudo-R32 (Monoclinic) Crystals

The extracellular domain of immunodeficiency virus gp41 protein: Expression inEscherichia coli, purification, and crystallization

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