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The crystallographic structure of Panicum Mosaic Virus (PMV).

Published on Jan 1, 2013in Journal of Structural Biology3.75
· DOI :10.1016/j.jsb.2012.10.012
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)
Cite
Abstract
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 Tobacco Necrosis Virus (TNV), of ∼20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca ++ ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1–53, 1–49 and 1–21 of the A, B and C subunits, respectively, and the four C-terminal residues (239–242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent “arm” that intertwines with symmetry equivalent “arms” at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A–B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.
  • References (58)
  • Citations (6)
Cite
References58
Newest
Published on Apr 14, 2012in International Tables for Crystallography
Michael G. Rossmann107
Estimated H-index: 107
(Purdue University),
Eddy Arnold41
Estimated H-index: 41
(RU: Rutgers University)
Noncrystallographic symmetry (NCS) occurs when symmetry operations are true only within a confined envelope, as opposed to being valid throughout the essentially infinite crystal lattice. Computationally, it is useful to define the molecular symmetry with reference to an arbitrary cell (the ‘h-cell’) with the relationship Xn = [Rn]X1 (n = 1, N). Then the assembly of N NCS equivalent objects can be moved into the actual crystal (the ‘p-cell’) using the relationship Y = [E]X. Hence each of the N u...
Published on Oct 1, 2011in Journal of Molecular Biology5.07
Stephen W. Lane2
Estimated H-index: 2
(University of Leeds),
Caitriona Dennis8
Estimated H-index: 8
(University of Leeds)
+ 4 AuthorsSimon E V Phillips S E42
Estimated H-index: 42
(University of Leeds)
Abstract A codon-optimised gene has been expressed in Escherichia coli to produce the coat protein (CP) of the Satellite Tobacco Necrosis Virus. This protein assembles in vivo into capsids closely resembling those of the T = 1 wild-type virus. These virus-like particles (VLPs) package the recombinant mRNA transcript and can be disassembled and reassembled using different buffer conditions. The X-ray crystal structure of the VLP has been solved and refined at 1.4 A resolution and shown to be very...
Published on Jan 1, 2009in Nucleic Acids Research11.15
Mauricio Carrillo-Tripp9
Estimated H-index: 9
(UM: University of Michigan),
Craig M. Shepherd4
Estimated H-index: 4
(UM: University of Michigan)
+ 6 AuthorsVijay S. Reddy29
Estimated H-index: 29
(UM: University of Michigan)
VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU)...
Published on Nov 1, 2007in Nature Protocols11.33
Axel T. Brunger101
Estimated H-index: 101
(Stanford University)
Version 1.2 of the software system, termed Crystallography and NMR system (CNS), for crystallographic and NMR structure determination has been released. Since its first release, the goals of CNS have been (i) to create a flexible computational framework for exploration of new approaches to structure determination, (ii) to provide tools for structure solution of difficult or large structures, (iii) to develop models for analyzing structural and dynamical properties of macromolecules and (iv) to i...
Published on Aug 1, 2006in Virology2.66
Debora L. Makino5
Estimated H-index: 5
(UCI: University of California, Irvine),
John Day10
Estimated H-index: 10
(UCI: University of California, Irvine)
+ 1 AuthorsAlexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine)
Three new crystal forms of satellite panicum mosaic virus (SPMV) were grown and their structures solved from X-ray diffraction data using molecular replacement techniques. The crystals were grown under conditions of pH and ionic strength that were appreciably different then those used for the original structure determination. In rhombohedral crystals grown at pH 8.5 and low ionic strength PEG 3350 solutions, Fourier syntheses revealed segments, ten amino acid residues long, of amino-terminal pol...
Published on Jan 1, 2006in International Tables for Crystallography
Kam Y. J. Zhang27
Estimated H-index: 27
(Fred Hutchinson Cancer Research Center),
Kevin Cowtan26
Estimated H-index: 26
(Ebor: University of York),
Peter Main7
Estimated H-index: 7
(Ebor: University of York)
Published on Apr 4, 2005in Archives of Virology2.26
J. M. S. Cardoso3
Estimated H-index: 3
(CSIC: Spanish National Research Council),
Maria do Rosário Félix6
Estimated H-index: 6
(University of Évora)
+ 1 AuthorsSolange Oliveira24
Estimated H-index: 24
(University of Évora)
The complete nucleotide sequence of a virus isolated from Olea europaea L. (GP isolate), previously identified as an isolate of Tobacco necrosis virus D (TNV-D) based on its coat protein sequence, was determined. The viral RNA genome consists of 3683 nucleotides and contains five open reading frames. The putative RNA-dependent RNA polymerase shows 91.2% amino acid identity with that of an isolate of Olive latent virus 1 (OLV-1) and the coat protein reveals highest sequence identity with that of ...
Published on Apr 1, 2005in Virology2.66
Steven B. Larson13
Estimated H-index: 13
(UCI: University of California, Irvine),
Robert W. Lucas8
Estimated H-index: 8
(UCI: University of California, Irvine)
+ 1 AuthorsAlexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine)
Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded ...
Published on Apr 1, 2005in BioEssays4.40
Alexander McPherson1
Estimated H-index: 1
Self-assembly processes of crystallization, micelle formation and virus assembly, by their creation of geometric order from disordered components, represent first-order phase transitions that arise through the formation of partially ordered intermediates. The self-assembly of protein subunits into the geometric shells of polyhedral viruses may proceed through formation of reverse micelles, and be driven by condensation of encapsidated nucleic acid complexed with the amino terminal polypeptides o...
Published on Mar 1, 2005in Virus Research2.74
Maria do Rosário Félix5
Estimated H-index: 5
(University of Évora),
Joana M. S. Cardoso4
Estimated H-index: 4
+ 1 AuthorsMaria Ivone E. Clara5
Estimated H-index: 5
(University of Évora)
Abstract An Olive latent virus 1 isolate designated GM6, obtained from a Portuguese olive tree, was characterized and the coat protein gene sequenced and analysed. The purified virus particles showed to be isometric with ca. 30 nm in diameter and contained a single-stranded RNA species with ca. 3.7 kb. The dsRNA profile obtained from infected tissues showed three major species with ca. 3.7, 1.5 and 1.3 kbp. SDS-PAGE analysis revealed a major peptide with an apparent molecular mass of 32 kDa iden...
Cited By6
Newest
Published on Feb 19, 2019in bioRxiv
Michael J. Tisza2
Estimated H-index: 2
(NIH: National Institutes of Health),
Diana V. Pastrana23
Estimated H-index: 23
(NIH: National Institutes of Health)
+ 21 AuthorsPatricia A. Pesavento25
Estimated H-index: 25
(UC Davis: University of California, Davis)
Virologists have posited the existence of millions of distinct viral species, but fewer than 9000 viral species are catalogued in GenBank9s RefSeq database. We selectively enriched for and amplified the genomes of circular DNA viruses in over 70 animal samples, ranging from cultured soil nematodes to human tissue specimens. Over 2500 complete circular genomes, each representing a new viral taxon, were assembled, thoroughly annotated, and deposited in GenBank. The new genomes belong to dozens of ...
Published on Jul 1, 2017in Biophysical Journal3.67
Sandro Bottaro12
Estimated H-index: 12
(UCPH: University of Copenhagen),
Kresten Lindorff-Larsen34
Estimated H-index: 34
(UCPH: University of Copenhagen)
Abstract We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the re...
Published on Dec 1, 2015in Scientific Reports4.01
Chun-Yan Wang3
Estimated H-index: 3
,
Qinfen Zhang15
Estimated H-index: 15
+ 4 AuthorsChuan-Xi Zhang28
Estimated H-index: 28
Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 A and 8 A resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction ...
Published on Nov 1, 2015in Virology2.66
Chun-Yan Wang3
Estimated H-index: 3
(ZJU: Zhejiang University),
Qin-Fen Zhang1
Estimated H-index: 1
(CAS: Chinese Academy of Sciences)
+ 5 AuthorsChuan-Xi Zhang28
Estimated H-index: 28
(ZJU: Zhejiang University)
Maize chlorotic mottle virus (MCMV) is the only member of the Machlomovirus genus in the family Tombusviridae. Here, we obtained the Cryo-EM structure of MCMV by single particle analysis with most local resolution at approximately 4 A. The Cα backbone was built based on residues with bulky side chains. The resolved C-terminus of the capsid protein subunit and obvious openings at the 2-fold axis demonstrated the compactness of the asymmetric unit, which indicates an important role in the stabilit...
Published on Jan 2, 2015in Crystallography Reviews2.67
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 whi...
Steven B. Larson13
Estimated H-index: 13
(UCI: University of California, Irvine),
John Day10
Estimated H-index: 10
(UCI: University of California, Irvine),
Alexander McPherson53
Estimated H-index: 53
(UCI: University of California, Irvine)
Satellite tobacco mosaic virus (STMV) is among the smallest viruses, having 60 identical subunits arranged with T = 1 icosahedral symmetry. Its crystal structure was solved at 290 K and was refined using, in part, crystals grown in microgravity. Electron-density maps revealed nearly 57% of the genomic ssRNA. Using six flash-cooled crystals, diffraction data were recorded to 1.4 A resolution and independent refinements of the STMV model were carried out versus the previous 1.8 A resolution data r...
Debora L. Makino5
Estimated H-index: 5
(MPG: Max Planck Society),
Elena Conti46
Estimated H-index: 46
(MPG: Max Planck Society)
The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3′ degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Several structures of subcomplexes of eukaryotic exosomes or related prokaryotic exosome-like complexes a...