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Jean-Yves Sgro
Inst. for Mol.Virology
731B Bock Labs
1525 Linden Drive Madison, WI 53706

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Magazine and Book Covers
Jean-Yves Sgro, Ph.D.
covers legend reference

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Journal Cover (Copyright © 2013):

legend: An HPV virion similar in structure to HPV18 (PDB 3IYJ - bovine papilloma) is shown radially colored to enhance the surface topography perception. Local plots derived from the reanalysis of ChIP-seq and RNA-seq datasets from HeLa-S3 cells show peaks in portrayed region of the HPV18 genome (red/blue gene map at top) for: Histone modifications, transcription factor binding, and RNA transcription. See Johannsen and Lambert for details.

Image Credits: UCSF Chimera virion image by Dr. J.Y. Sgro, UW-Madison | Reanalysis plots by Prof. Eric Johannsen

X-ray crystallography data: Wolf, M., Garcea, R.L., Grigorieff, N., Harrison, S.C. (2010) Subunit interactions in bovine papillomavirus. Proc.Natl.Acad.Sci.USA 107: 6298-6303
PubMed

VIROLOGY Volume 445, Issues 1-2, Pages 1-244 (October 2013) Special Issue: The Papillomavirus Episteme

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Journal Cover (Copyright © 2013):

legend: PyMOL-rendered image of human Seneca Valley Virus-001 (Protein Data Bank ID: 3cji) illustrating virion topography by radial depth-cueing.

Image: Jean-Yves Sgro/ University of Wisconsin-Madison

X-ray crystallography data: Venkataraman, S., Reddy, S.P., Loo, J., Idamakanti, N., Hallenbeck, P.L., Reddy, V.S. (2008) Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus. Structure 16: 1555-1561
PubMed

PHARMACY Purchasing & Products (www.pppmag.com)

July 2013
VOL 10, No 10

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Journal Cover (Copyright © 2010):

legend: About the cover
On our cover this month, a QuteMol-rendered image of human rhinovirus 3 (pdbID: 1rhi) illustrates the virion topography. The surface depressions around the 5-fold symmetry axes contribute to receptor binding (ICAM-1). Higher regions on the capsid surfaces encode the immunogenic serotype. An example of an HRV RNA genome secondary structure iscolored according to predicted base-pairing fidelity. This image highlights this month's emphasis on viruses in asthma. In our Clinical Reviews series, David Jackson andS ebastian L. Johnston (p1178) discuss the role that viruse splay in asthma exacerbations. For our Mechanisms series, Ann C. Palmenberg et al (p1190) provide ananalysis of human rhinovirus genome sequences and the implications for future treatments and research. A Current Perspectives article by Peter D. Sly et al. (p 1202) reviews the latest evidence regarding whether viral infections early in life cause asthma. To find these and other articles relevant to this month's theme, look for the red starburst icon in the Table of Contents.
The components contained in this month's cover were created by H. Adam Steinberg and Jean-Yves Sgro, University of Wisconsin-Madison. Adapted for thecover by JDI, LLC. The Editors also wish to thank James Gern and Ann Palmenberg for their assistance.
© 2010 American Academy of Allergy, Asthma & Immunology

X-ray crystallography data: Zhao, R., Pevear, D.C., Kremer, M.J., Giranda, V.L., Kofron, J.A., Kuhn, R.J., Rossmann, M.G. (1996) Human rhinovirus 3 at 3.0 A resolution. Structure 4: 1205-1220
PubMed

The Journal of Allergy and Clinical Immunology
(http://www.jacionline.org)

- Volume 125, Issue 6, Pages 1175-1476 (June 2010)


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Journal Cover (Copyright © 2009):

legend: QuteMol-rendered image of human rhinovirus 3 (Protein Data Bank ID: 1rhi) illustrating virion topography. Red, blue, and yellow denote the three major surface capsid proteins; examples of RNA regional motifs are colored according to predicted base-pairing fidelity. Sequence diversity within the major surface proteins contributes to the wide range of immunogenic serotypes characteristic of the "common cold." See page 55.

Image: H. Adam Steinberg and Jean-Yves Sgro/ University of Wisconsin-Madison

X-ray crystallography data: Zhao, R., Pevear, D.C., Kremer, M.J., Giranda, V.L., Kofron, J.A., Kuhn, R.J., Rossmann, M.G. (1996) Human rhinovirus 3 at 3.0 A resolution. Structure 4: 1205-1220
PubMed

Science (www.sciencemag.org)

3 APRIL 2009
VOL 324, ISSUE 5923, PAGES 1-130

Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, Fraser-Liggett CM, Liggett SB.
Science 3 April 2009: Vol. 324. no. 5923, pp. 55 - 59
DOI: 10.1126/science.1165557


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Journal Cover (Copyright © 2009):

Cover Legend: Shown are images of adenovirus (top center), polyomavirus (bottom right) and papillomavirus (bottom left). Images were created by Dr. Jean-Yves Sgro, Ph.D., Senior Scientist, Institute for Molecular Virology, University of Wisconsin-Madison with visualization software VMD. The following coordinate information was accessed through VIPERdb2. For adenovirus: PDB ID: 2bld; (Fabry et al., 2005, Embo J. 24:1645-1654); for polyomavirus: PBD ID: 1sid (Stehle and Harrison 1996, Structure 4:183-194); for papillomavirus: PBD ID: 1l0t (Modis et al., 2002, EMBO J. 21:4754-62). For adenovirus, spike proteins are not visualized. For papillomavirus, the carbon-alpha backbone coordinates were converted to full coordinates with software Sybyl (Tripos, Inc.).

Virology (Elsevier)

Volume 384, Issue 2, Pages 255-414 (20 February 2009) Small Viruses, Big Discoveries: The Interwoven Story of the Small DNA Tumor Viruses

Edited by Paul F. Lambert


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Magazine Cover (Copyright © 2007):

legend: Human Papilloma Virus, radially depth cued, as solved by X-ray crystallography (Original Art Image © 2007 Jean-Yves Sgro, University of Wisconsin Institute for Molecular Virology)

Surface rendering from atomic coordinates (PDB ID 1L0T) is radially depth cued by color and was created with the program GRASP.

ATOMIC MODEL OF THE PAPILLOMAVIRUS CAPSID Modis, Y., Trus, B.L., Harrison, S.C.

Virus Image created by JY Sgro

NursingSpectrum (www.nurse.com)
Washington DC/ Mmaryland/ Virginia edition

Outcry Over HPV Vaccine Indicates Need for More Education

Joan Wilder
Monday March 26, 2007


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Magazine Cover (Copyright © 2007):

legend: Human Papilloma Virus, radially depth cued, as solved by X-ray crystallography (Original Art Image © 2007 Jean-Yves Sgro, University of Wisconsin Institute for Molecular Virology)

Surface rendering from atomic coordinates (PDB ID 1L0T) is radially depth cued by color and was created with the program GRASP.

ATOMIC MODEL OF THE PAPILLOMAVIRUS CAPSID Modis, Y., Trus, B.L., Harrison, S.C.

Virus Image created by JY Sgro

NursingSpectrum (www.nurse.com)
Greater Philadelphia Tri-State edition

Outcry Over HPV Vaccine Indicates Need for More Education

Joan Wilder
Monday March 26, 2007


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Book Cover (Copyright © 2006, Wiley):

legend: Simian Virus 40, radially depth cued, as solved by X-ray crystallography (Original Art Image © 2006 Jean-Yves Sgro, University of Wisconsin Institute for Molecular Virology)

Atom rendering from atomic coordinates (PDB ID 1SVA) is radially depth cued by color and was created with the program VMD.

Stehle, T., Gamblin, S.J., Yan, Y., Harrison, S.C. (1996) The structure of simian virus 40 refined at 3.1 A resolution. Structure 4: 165-182

Virus Image created by JY Sgro

Fundamentals of Molecular Virology
Publisher: John Wiley & Sons, Inc.; 1 edition (November 10, 2006)
ISBN-10: 0471351512
ISBN-13: 978-0471351511
Paperback: 432 pages

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legend: Hepatitis B virus, rdially depth cued, as solved by X-ray crystallography (Image © 2004 Jean-Yves Sgro, University of Wisconsin Institute for Molecular Virology)

Atom rendering from atomic coordinates (PDB ID 1QGT) is radially depth cued by color and was created with the program RASMOL.

Wynne, S.A., Crowther, R.A., Leslie, A.G. (1999) The crystal structure of the human hepatitis B virus capsid. Mol. Cell 3: 771-780

Virus Image created by JY Sgro

HEPATOLOGY, VOLUME 44, NUMBER 2, AUGUST 2006
.


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legend:Molecular surface of Poliovirus Type 1 Mahoney, rdially depth cued, as solved by X-ray crystallography (Image © 1999 Jean-Yves Sgro, University of Wisconsin Institute for Molecular Virology)

Surface rendering from atomic coordinates (PDB ID 2PLV) is radially depth cued by color and was created with the program GRASP.

Filman, D. J., Syed, R., Chow, M., Macadam, A. J., Minor, P. D., Hogle, J. M.: Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus. EMBO J 8 pp. 1567 (1989)

Virus Image created by JY Sgro

Occurrence and Distribution of Enteric Viruses in SHallow Ground Water and Factors Affecting Well Vulnerability to Microbiological Contamination in Worcester and Wicomico Counties, Maryland
. Banks, W.S.L. and Klohe C.A. (US Geological Survey) and Batigelli D.A. (Wisconsin State Laboratory of Hygiene)
Water-Resources Investigations Report 01-4147
In cooperation with the Maryland Department of the Environment.
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Cover photograph (Copyright © 2001, American Society for Microbiology. All rights reserved.): Structure of the cucumber necrosis virus (CNV) particle (T=3 icosahedron), showing areas of the capsid important in fungal vector recognition. Areas in yellow correspond to amino acid residues in the particle quasi-threefold axis that are mutated in naturally occurring CNV transmission mutants. The mutations also affect attachment to the outer membrane of the fungal zoospore, suggesting a role for these sites in receptor recognition. Three-dimensional coordinates for the CNV structure were obtained by homology modeling, using tomato bushy stunt virus coordinates and the program MODELLER. Surface rendering from atomic coordinates is radially depth cued by color and was created with the program GRASP.


Virus Image created by JY Sgro
Journal of Virology
volume 75 June 2001 Issue 12
The American Society for Microbiology

Related article: Kishore Kakani,Jean-Yves Sgro, and D'Ann Rochon (2001) Identification of Specific Cucumber Necrosis Virus Coat Protein Amino Acids Affecting Fungus Transmission and Zoospore Attachment J. Virol. 75(12): 5576-5583


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legend: Principios de virología

FRONT COVER: Many virus images. Sizes are not to relative scale.

The larger image is that of foot-and-mouth disease virus (FMDV), shown as radially depth cued. In reality this virus is not larger than the other viruses represented here. The red surface represents the location of the highly antigenic loop (residues 134 - 157 on protein VP1) which was disordered in previous crystallographic attempts.

FMDV, PDB-ID: 1FOD:
D.LOGAN, R.ABU-GHAZALEH, W.BLAKEMORE, S.CURRY, T.JACKSON, A.KING, S.LEA, R.LEWIS, J.NEWMAN, N.PARRY, D.ROWLANDS, D.STUART, E.FRY Structure of a major immunogenic site on foot-and-mouth disease virus. Nature 362 566, 1993.

BACK COVER: 2 stereo pairs, top pair depicts FMDV (virus de la fiebre aftosa), bottom pair depicts poliovirus structure. Both viruses have a similar diameter of about 30 nm.

Principios de virología
© 2000
ISBN:958-655-449-X
Jorge Ossa Londoño Editor,
Medellín, Colombia.

Language: Spanish

Links:

  • Aspectos de la Universidad Colombiana
  • Alumni Profile, (UW-Madison)

    e-mail: jeossa@catios.udea.edu.co



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    legend: Largest and smallest complete viral particles solved by X-Ray crystallography. Both structures are reprented here to scale.

    The larger structure is simian virus 40 (PDB entry 1SVA, Stehle et. al. 1996), a Polyomavirus from the Papovaviridae family. The non-enveloped icosahedral particles, ~45 nm in diameter contains the circular dsDNA genome. 72 pentameric capsomers are arrange on a T=7d icosahedral lattice, 12 strict pentamers at the icosahedral vertices have only 5 neighbouring capsomers while the other and 60 pentameric capsomers are arranged in hexamers. View is along an icosahedral 2-fold axis of symmetry.

    The small structure is that of satellite tobacco necrosis virus (PDB entry 2STV, Unge et. al. 1980). The non-enveloped icosahedral particles, ~17 nm in diameter contains the linear ssRNA genome. 60 proteins are arranges on a T=1 icosahedral lattice. View is along an icosahedral 5-fold axis of symmetry.

    T.STEHLE,S.J.GAMBLIN,Y.YAN,S.C.HARRISON The structure of simian virus 40 refined at 3.1 A resolution STRUCTURE (LONDON) 4, 165 1996

    T.UNGE,L.LILJAS,B.STRANDBERG,I.VAARA,K.K.KANNAN, K.FRIDBORG,C.E.NORDMAN,P.J.LENTZ *JUNIOR Satellite tobaco necrosis virus structure at 4.0 A resolution NATURE 285,373 1980

    Archives of Virology
    All 1999 volumes.
    ISSN 0304-8608
    Springer-Verlag Wien

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    legend: Coxscakievirus B3 image is a computer representation derived fromx-ray coordinates (Mucklebauer et al. Structure 3:653, 1995). The PDB ENTRY for the virus is 1COV. The GRASP protein molecular surface is radially depth-cued to visually highlight surface features. The canyon is clearly evident. Note that the canyons are not continuous around the 5-fold icosahedral axes. (Courtesy of Dr. Jean-Yves Sgro, University of Wisconsin-Madison; sgro@rhino.bocklabs.wisc.edu).

    Photomicrographs of 0.6 micron thick hemotoxylin and eosin stained sections of heart (above) and pancreas (below) taken from a C3H/HeJ male mouse, 10 days post-inoculation with the cardiovirulent wild-type strain of CVB3, CVB3/DO. Note significant and widespread regions of necrosis and calcification in heart section typical of results induced by infection with a cardiovirulent CVB3. Pancreas has sustained severe damage to acinar cells. Original magnification x100.

    The Coxsackie B Viruses
    S. Tracy, N.M. Chapman and B.W.J. Mahy (Eds)
    Springer
    1997
    ISSN 0070-217X
    ISBN 3-540-62390-6
    Library of Congress Catalog Card Number 15-12910

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    legend: Computer-generated image of poliovirus type 1 Mahoney strain derived from X-ray coordinates (PDB entry 2PLV, Hogle et al.) showing a virion oriented along one of twelve icosahedral 50fold symmetry axes. Image generated by J.-Y. Sgro with the program GRASP on Silicon Graphics. There are three articles about poliovirus in this issue: M.-M. Georgescu et al. (pages 1819-1828), B. Rombaut and J.P. M. Jore (pages 1829-1832) and F. J. M. Kuppeveld et al. (pages 1833-1840).

    Image represents poliovirus type 1 Mahoney (X-ray data Hogle et al., 1985, Science 229: 1358) seen along one icosahedral 5-fold axis. Down in the depression around the 5-fold axis the small yellow sticks represent a visible portion of the "pocket factor". In most rhinoviruses this pocket entry would be blocked by the C-terminal end of the VP3 protein "hanging" above the pore entrance.
    The image in radially depth cued to enhance toppographical perception of the surface. Lighter colors are more prominents, darker colors represents areas closer to the virion center.
    Created with Grasp (A.Nicholls) on Silicon Graphics from PDB published coordinates (PDB entries 2PLV).
    Image created by JY Sgro.

    Journal of General Virology
    Volume 78 Part 8
    August 1997

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    No legend.
    Image represents halved virion particles of Theiler's virus BeAn (green) and DA (orange) strains, showns side by side for comparison, created with Grasp on Silicon Graphics from PDB published coordinates (PDB entries 1TME (DA) and 1TMF (BeAn)).
    Image created by JY Sgro
    Journal of General Virology
    Off-Print promotional cover
    1997


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    Computer graphics of the three-dimensional structure of bean pod mottle virus. The surface of virions has been radially depth-cued to enhance depiction of surface topography. Virions on the left appear in various orientations; prominent structures protrude at axes of 5-fold symmetry (yellow); deep depressions occur at axes of 2-fold symmetry; and small surface ridges are visible at axes of 3-fold symmetry. The virion at the right has been sliced through is center to reveal interior features. Capsid protein atoms are delineated as blue spheres to show the capsid thickness (<10 Å at 2-fold axes, > 40 Å at 5-fold axes). About 20% of the virion RNA was detected; it appears as trefoils (pink) at axes of 3-fold symmetry. In the foreground an edge of a virion appeats at close range. The structure of this virus was solved in the laboratory of J.E. Johnson, then at Purdue University [Chen et al., Science 245:154-159 (1989)]. The illustration was created on a Silicon Graphics Workstation, using the program GRASP as developped by Anthony Nicholls of Columbia University. The image was composed and produced by Jean-Yves Sgro of the Institute for Molecular Virology, University of Wisconsin, 1525 Linden Drive, Madison, Wisconsin, 53706-1596 USA. Archives of Virology
    All 1996 volumes.
    ISSN 0304-8608
    Springer-Verlag Wien

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    Artistic rendering of a Mengo virion releasing its single stranded RNA genome after infecting a cell. Four kinds of viral coat proteins assemble following icosahedral symmetry o form a shell around the genome. The icosahedral 5-fold axis of symmetry is easily recognized at the center of the pentamers, star shaped raised surfaces. See "Using Viral Genes to Fight Disease," p. 1050.
    Image created by JY Sgro
    BIOTECHNOLOGY
    volume 13 October 1995 Number 10
    ISSN 0733-222X
    Nature Publishing Co., owned by Nature America, Inc., a subsidiary of Macmillan Magazines of London.

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    Computer graphics representation of the virion of human rhinovirus 14 along the icosahedral 3-fold axis of symmetry, highlighting the topographic details of the surface. Lighter colored structures are situated further away from the virion center, showing that the 5-fold axis region is the most prominent feature. The "canyon" is clearly seen as a dark blue depression around the 5-fold axis and is the binding site for the cellular receptor ICAM-1. A depression is visible at the icosahedral 2-fold axis of symmetry (equidistant between two 5-fold vertices), but has no known role. Antibody binding sites determined by escape mutations are shown in magenta and clearly appear in more exposed (white or light blue) areas on "domes" and "ridges", suggesting that the dark and blue areas are not within the reach of antibodies.
    Image created by JY Sgro
    Medical Virology
    David O. White
    Frank J. Fenner
    Academic Press, Inc.
    ISBN 0-12-746642-8
    1994

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    Image created by JY Sgro from VSurf Data (VSurfProgram from Michael Rossamnn) and visualized with FRODO on an Evans & Sutherland PS390 series workstation.

    NIAID
    Report of the Task Force on Microbiology and Infectious Diseases
    U.S. Department of Health and Human Services
    Public Health Service
    National Institute of Health
    1992