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A guide to the crystallographic analysis of icosahedral viruses

Published on Jan 2, 2015in Crystallography Reviews 2.67
· DOI :10.1080/0889311X.2014.963572
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine),
Steven B. Larson13
Estimated H-index: 13
(UCI: University of California, Irvine)
Determining the structure of an icosahedral virus crystal by X-ray diffraction follows very much the same course as conventional protein crystallography. The major differences arise from the relatively large sizes of the particles, which significantly affect the data collection process, data processing and management, and later, the refinement of a model. Most of the other differences are due to the high 5 3 2 point group symmetry of icosahedral viruses. This alters dramatically the means by which initial phases are obtained by molecular substitution, extended to higher resolution by electron density averaging and density modification, and the refinement of the structure in the light of high non-crystallographic symmetry. In this review, we attempt to lead the investigator through the various steps involved in solving the structure of a virus crystal. These steps include the purification of viruses, their crystallization, the recording of X-ray diffraction data, and its reduction to structure amplitudes. ...
  • References (152)
  • Citations (1)
Published on Jan 2, 2015in Crystallography Reviews 2.67
Michael G. Rossmann107
Estimated H-index: 107
(Purdue University)
My first experiences with crystallography were as a graduate student at the University of Glasgow determining the structure of aromatic hydrocarbons using only primitive hand calculation techniques. I had my first experience using electronic computers as a post-doc in the lab of William Lipscomb in Minnesota. That gave me a good preparation for the structure determination of haemoglobin with Max Perutz in Cambridge. The discovery of the conserved globin fold had a major impact on my subsequent a...
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine),
Bob Cudney3
Estimated H-index: 3
© 2014 International Union of Crystallography. For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for ...
Jimin Wang44
Estimated H-index: 44
(Yale University),
Richard A. Wing4
Estimated H-index: 4
(Rockefeller University)
Overwhelming evidence exists to show that the inclusion of weak-intensity, high-resolution X-ray diffraction data helps improve the refinement of atomic models by imposing strong constraints on individual and overall temperature B factors and thus the quality of crystal structures. Some researchers consider these data to be of little value and opt to discard them during data processing, particularly at medium and low resolution, at which individual B factors of atomic models cannot be refined. H...
Published on Apr 1, 2014in Journal of Experimental Botany 5.36
Andrey G. Solovyev27
Estimated H-index: 27
(MSU: Moscow State University),
Eugene I. Savenkov26
Estimated H-index: 26
(SLU: Swedish University of Agricultural Sciences)
Compatible virus–host interactions depend on a suitable milieu in the host cells permitting viral gene expression, replication, and spread. During pathogenesis, viruses hijack the plant cellular machinery to access molecules, subcellular structures, and host transport pathways needed for infection. Vascular trafficking of virus transport forms (VTF) within the phloem is a crucial step in setting-up virus infection within the entire plant. Moreover, vascular trafficking is an essential step for t...
Published on Jan 1, 2014in Methods of Molecular Biology
Frank Sainsbury21
Estimated H-index: 21
(UQ: University of Queensland),
Pooja Saxena9
Estimated H-index: 9
(JIC: John Innes Centre)
+ 3 AuthorsGeorge P. Lomonossoff52
Estimated H-index: 52
(JIC: John Innes Centre)
The development of methods for the production of empty Cowpea mosaic virus (CPMV) virus-like particles (VLPs) that are devoid of RNA, eVLPs, has renewed promise in CPMV capsid technologies. The recombinant nature of CPMV eVLP production means that the extent and variety of genetic modifications that may be incorporated into the particles is theoretically much greater than those that can be made to infectious CPMV virions due to restrictions on viral propagation of the latter. Free of the infecti...
Published on Nov 1, 2013in FEBS Journal 4.74
Alexander Wlodawer65
Estimated H-index: 65
Wladek Minor40
Estimated H-index: 40
+ 1 AuthorsMariusz Jaskolski36
Estimated H-index: 36
(PAN: Polish Academy of Sciences)
The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from bein...
Kay Diederichs51
Estimated H-index: 51
(University of Konstanz),
P.A. Karplus5
Estimated H-index: 5
(OSU: Oregon State University)
In macromolecular X-ray crystallography, typical data sets have substantial multiplicity. This can be used to calculate the consistency of repeated measurements and thereby assess data quality. Recently, the properties of a correlation coefficient, CC1/2, that can be used for this purpose were characterized and it was shown that CC1/2 has superior properties compared with ‘merging’ R values. A derived quantity, CC*, links data and model quality. Using experimental data sets, the behaviour of CC1...
Philip R. Evans41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology),
Garib N. Murshudov41
Estimated H-index: 41
(LMB: Laboratory of Molecular Biology)
Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point-group symmetry of the data and the likely space group. This can be performed with the program POINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry-related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling...
Published on Jan 1, 2013in Journal of Structural Biology 3.75
Debora L. Makino5
Estimated H-index: 5
(UCI: University of California, Irvine),
Steven B. Larson13
Estimated H-index: 13
(UCI: University of California, Irvine),
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine)
Abstract The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9 A resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P 2 1 with a = 411.7 A, b = 403.9 A and c = 412.5 A, with β = 89.7°. The asymmetric unit was two entire T = 3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacc...
Cited By1
Christian X. Weichenberger11
Estimated H-index: 11
(European Academy of Bozen),
Pavel V. Afonine29
Estimated H-index: 29
(LBNL: Lawrence Berkeley National Laboratory)
+ 1 AuthorsBernhard Rupp30
Estimated H-index: 30
(Innsbruck Medical University)
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinemen...