The online NY Times article still states (first sentence): "For the first time, researchers at an I.B.M. laboratory have captured a three-dimensional image of a virus (it is Tobacco Mosaic Virus)." I suppose one could discount x-ray methods (via phasing & subsequent computational image reconstruction) as producing "images", if one were so inclined. But, to my knowledge, the first WAS indeed (Tomato) Bushy Stunt Virus:
http://www.ncbi.nlm.nih.gov/pubmed/834302
Nature. 1977 Feb 10;265(5594):509-13.
Tomato bushy stunt virus at 5.5-A resolution.
Winkler FK, Schutt CE, Harrison SC, Bricogne G.
The coat of tomato bushy stunt virus is built from protein subunits having rigid domains connected by a flexible hinge. Two states of the hinge are present in the T=3 icosahedral structure. Each subunit has a binding site for RNA on its inner surface.
Followed by (which interestingly, PubMed doesn't abstract!):
Nature 276, 368 - 373 (23 November 1978); doi:10.1038/276368a0
Tomato bushy stunt virus at 2.9 Å resolution
S. C. Harrison‡, A. J. Olson‡, C. E. Schutt*‡, F. K. Winkler†‡ & G. Bricogne§
‡Gibbs Laboratory, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
§MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
*Present address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK.
†Present address: EMBL, Heidelberg, FRG.
The polypeptide chain of a TBSV subunit folds into two domains, connected by a hinge, and a flexibly-linked N-terminal arm. Sixty of the 180 N-terminal arms inter-digitate in groups of three, in an unexpected mode of protein association. The remaining 120 arms are not uniquely positioned with respect to the rest of the subunit. RNA is also not uniquely fixed to sites on the major domains.
The last one really counts, to me, as an "image".
Michael Rossmann & group were close behind with Southern Bean Mosaic Virus (again not in PubMed):
Nature 286, 33 - 39 (03 July 1980); doi:10.1038/286033a0
Structure of southern bean mosaic virus at 2.8 Å resolution
Celerino Abad-Zapatero, Sherin S. Abdel-Meguid, John E. Johnson, Andrew G. W. Leslie*, Ivan Rayment†, Michael G. Rossmann, Dietrich Suck‡ & Tomitake Tsukihara§
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
Present addresses: * Biophysics Section, Blackett Laboratory, Imperial College of Science and Technology, Prince Consort Road, London SW7 2BZ, UK; † Structural Biology Laboratory, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02154; ‡ European Molecular Biology Laboratory, Postfach 10 22 09, 69 Heidelberg 1, FRG; § Department of Chemistry, Faculty of Engineering, Tottori University, Koyama-cho, Tottori 680, Japan.
X-ray diffraction studies reveal that the polypeptide chain of the southern bean mosaic virus protein subunit has a fold closely similar to the shell domain of tomato bushy stunt virus. The protruding domain of tomato bushy stunt virus is absent in southern bean mosaic virus. The tertiary structure observed in these viruses may be particularly suitable for the formation of the protein coat in small, spherical, RNA-containing, plant viruses.
There were also a number of publications in, e.g., the Cold Spring Harbor Symposium of Quantitative Biology, along the way to these structures.
Dave
P.S. - The first structure of TMV (not the "disk", but the virus) at comparable resolution is, to my knowledge, the work of Gerald Stubbs & colleagues (quite a tour de force...fiber diffraction):
http://www.ncbi.nlm.nih.gov/pubmed/2769760
J Mol Biol. 1989 Jul 20;208(2):307-25.Click here to read Links
Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.
Namba K, Pattanayek R, Stubbs G.
Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235.
The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites.
David Borhani, Ph.D.
D. E. Shaw Research, LLC
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
[log in to unmask]
212-478-0698
http://www.deshawresearch.com
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Christoph Best
> Sent: Tuesday, January 13, 2009 9:20 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] IBM / MRI / tobacco mosaic virus
>
> Patrick Loll <[log in to unmask]> writes:
> > I just read an appalling article in the science section of
> today's NY Times
> > that refers to a new magnetic resonance force microscope
> developed at IBM. The
> > story states "For the first time, researchers at an IBM
> laboratory have
> > captured a three-dimensional image of a virus."
>
> They might have thought of a 3D image of a _single_ virus - that would
> explain the oblique reference to Electron Microscopy in the article
>
> "But these techniques are more destructive of biological samples
> because they send a stream of electrons at the target in
> order to get
> an image"
>
> (though the article refers to STM and AFM, for which this is not
> true). Good EM tomograms of single viruses have been around for a few
> years now (and much much longer using icosahedral
> reconstruction), e.g.
>
> http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1155_visualization.html
>
> > The same article states that this instrument can be used to
> "...look at the
> > proteins that make up the basic DNA structure...[sic]". Sigh.
>
> That's funny, this is already corrected in the online version
>
> http://www.nytimes.com/2009/01/13/science/13mri.html?ref=science
>
> -Christoph
>
> PS: The article was written by their Silicon Valley
> correspondent - bad luck
> for IBM Research that they are, after all, a computer company.
>
> --
> | Christoph Best <[log in to unmask]>
> http://www.ebi.ac.uk/~best
> | European Bioinformatics Institute, Cambridge, UK
> +44-1223-492649
>
