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Color Plates

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Figures

Image of Color Plate 1a [chapter 3]

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Color Plate 1a [chapter 3]

A schematic diagram created using MOLSCRIPT (58) representing VP1 of HRV16, showing the binding site of the pocket factor (ball-and-stick representation) and the WIN antiviral compounds (pale blue). A cation on the fivefold axis is shown in yellow. The N termini of VP1, VP3, and VP4 intetact around the fivefold axis. One copy of each of VP1 and the N termini of VP3 and VP4 arc shown as blue, red, and green ribbon diagrams, respectively. The myristoylated N terminus of VP4 is labeled (MYR). Reprinted with permission from Hadfield et al. (39).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 1b

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Color Plate 1b

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 2 [chapter 3]

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Color Plate 2 [chapter 3]

Different types of teptesentations possible with “roadmaps.” The triangle represents one icosahedral asymmetric unit. The viral surface is projected onto a plane perpendicular to one icosahedtal axis placed normal to the page. (A) Surface topographies of various picornaviruses: HRV1A (56), HRV14 (87), poliovirus 1 Mahoney (51), and mengovirus (74). The colors show the distance from the viral center, where blue is “low lying seas” and white is “high mountains.” Images were supplied by Dr. Jean-Yves Sgro (University of Wisconsin, Madison, http://www.bocklabs.wisc.edu/topo.html). Reprinted with permission from Rotbart and Kirkegaard (90). (B) The surface of HRV14 showing the exposed areas of each amino acid in one icosahedral asymmetric unit. Residues involved in neutralizing immunogenic sites are hatched. Reprinted with permission from Rossmann and Palmenberg (89).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 3 [chapter 3]

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Color Plate 3 [chapter 3]

Antiviral compounds hound to picornaviruses: (A) Diagrammatic representation of an antiviral compound binding within the -barrel of VP1. (B) Electron density, at 3.0 Å resolution, of HRV14 complexed with the antiviral agent WIN 52084. This and telated compounds stabilize the virus to inhibit uncoating and can also inhibit attachment. Shown is the molecular interpretation of the electron density. The compound consists of a 4-oxazaolinylphenoxy group linked to a 3-methylisoxazole group by a seven-membered aliphatic chain. The compound binds into a hydrophobic pocket in VP1 that is lined by residues that are moderately well conserved among picornaviruses. Reprinted with permission from Smith et al. (98). (C) Chemical structure of pleconaril, the compound possibly to be matketed by ViroPharma, Inc.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 4 [chapter 4]

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Color Plate 4 [chapter 4]

Architecture of rhinovirus 14. A schematic of HRV14 is shown with the various NIm sites and canyon tegion labeled. VP1 to 3 are colored blue, green, and red, respectively. The four NIm sites are colored according to the scheme used in Color Plate 7A . The canyon regions are approximated by the black circles drawn around each fivefold axis.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 5 [chapter 4]

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Color Plate 5 [chapter 4]

Cryo-TEM analysis of HRV14 complexed with Fabl7, Fabl2, Fabl, and mAbl7. The reconstructions of Fabl7, Fabl, and Fabl2 are shown in panels A to C, respectively. The virus surface is colored gray, and the antibodies are highlighted with various colors. The fitting of Fabl7 and Fabl structures into the cryo-TEM electron density is shown in panels D and E. The view here is parallel to the canyon region with the fivefold axis on the left, the twofold axis on the right, and the RNA interior on the bottom. Panel F shows an overlay of the Fabl (green) versus Fabl2 (mauve) viewed from the fivefold axis toward the twofold axis. Reprinted from the (9) with permission from publisher.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 6 [chapter 4]

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Color Plate 6 [chapter 4]

Crystal structure of the Fabl7-HRV14 complex. The V, V, VPl, VP2, VP3, and VP4 C- backbones are represented by yellow, white, blue, green, red, and cyan, respectively. The differences in the Fabl2 and Fabl7 sequences are represented by mauve balls in the framework regions, and mutations in the CDR regions are represented by yellow balls. The view here is the same as that in Color Plate 5D and E . Note the penetration of the Fab into the canyon and the extensive contact along the south wall (the right side of the central depression). Reprinted from the (9) with permission from publisher.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 7 [chapter 4]

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Color Plate 7 [chapter 4]

Stereo images of the various locations mapped onto the surface of HRV14. In panel A the NIm sites are mapped onto a portion of the HRV14 surface. The icosahedral asymmetric unit is denoted by the green triangle and the locations of the five- and twofold axes are labeled. Panel B shows the Fab 17 contact area in red. Panel C shows the surface locations of the two peptides used to elicit antibodies that exhibited cross-reactivity to several rhinovirus serotypes.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 8 [chapter 4]

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Color Plate 8 [chapter 4]

Pocket factor in the HRV14-Fabl7 complex. This figure shows the VPl strand immediately above the drug pocket that moves upon binding WIN drugs (A) and the pocket factor density observed in the Fab-HRV14 crystals structure. (A) The black cage represents the electron density of this region in the Fabl7-HRV14 crystal structure. The transparent mauve model is the native HRV14 structure, and the stick model (colored by atom type) is taken from the WIN-HRV14 structure. (B) The density beneath this conformational change with the WIN compound (represented by the multicolored ball and stick model) is shown as a positional reference. Some of the nearby side chains are represented by the blue ball and stick models.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 9 [chapter 8]

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Color Plate 9 [chapter 8]

(a) The ribbon diagram of ICAM-1 domains Dl and D2. The residues and loops that penetrate into the HRV canyon are colored white. Glu34, essential for LFA-1 binding, is shown in yellow. Note the elbow angle that telates the two domains, (b) Important contact residues for HRV and coxsackievirus A21 in the Dl domain. The -strands are labeled A through G. The amino acids identified as being in the virus-receptor interface are indicated by spheres. ICAM-1 residues in contact with HRV14 and HRV16 are colored blue, while ICAM-1 residues in contact with coxsackievirus A21 are indicated in red. Modified from the (2) with permission of the publisher.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 10 [chapter 8]

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Color Plate 10 [chapter 8]

(a) Cryo-EM image reconstructions of complexes between HRV14 or HRV16 and soluble D1D2 of ICAM-1 at 26 Å resolution, (b) Ribbon diagram showing the interaction of ICAM-1 (yellow) and HRV 16. HRV 16 proteins VP1, VP2, and VP3 are in blue, green, and red, tespectively. Two symmetry-related VPls and VP3s are shown. Some icosahedral symmetry elements and the boundary of an icosahedral asymmetric unit are shown.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 11 [chapter 17]

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Color Plate 11 [chapter 17]

Comparison of the structures of HAV 3C, -chymotrypsin, and PV1 3C. Secondary structural ribbon diagrams of HAV 3C (left), -chymotrypsin (centet), and PV1 3C (right). The N-tetminal -barrels are represented by the cyan-colored arrows, Cterminal -barrels by lilac arrows. The extensions in PV1 and HAV 3C to -strands bill and ell that do not form part of the -barrels are shown in gray; the corresponding region in chymotrypsin (the “methionine loop”) is also shown in gray. Helices are represented by green spiral ribbons and connecting loops by red tubes. The white segments in each of the representations denote the oxy-anion hole. The side chains of the catalytic residues (Set, His, and Asp in achymotrypsin; Cys, His, and Glu in PV1-3C; and Cys, His, H0, Asp, and Tyr in HAV 3C) are represented in each molecule. The Hisl61 (PV1) and Hisl91 (HAV) of the SI pockets of PV1 3C and HAV 3C that determine the cleavage specificity fot Gln in substrates are shown in light blue. All three molecules are represented from approximately the same vantage point.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 12a [chapter 17]

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Color Plate 12a [chapter 17]

Comparison of the active sites of (A) PV1 3C, (B) HAV 3C, and (C) HRV2 3C. (A) A computer-generated model of residues to of Ala-Lys-Val-Gln- Gly-Pro (cleavage site between 3B and 3C of the polyprotein) in the active site of PV1-3C. The atomic color coding for the substrate is blue, nitrogen; orange, oxygen; and gray, carbon. For the enzyme, color coding is blue, nitrogen; red, oxygen; the residues forming subsites , , , , and are represented by different colors for the C atoms. Hydrogen bonds are designated by dashed lines between donor and acceptot atoms. Three close-ups of the subsites are shown below; and (left); (center); and (right). (B) A view of the computer-generated HAV-3C/substrate model. The color schemes are the same as those shown in panel A. The substrate was generated from the residues of the cleavage site between VPl and 2B of the HAV polyprotein (Leu-Phe-Ser-Gln-Ala-Lys). Hydrogen bonds are represented by dashed lines between donor and acceptor atoms. The three lower portions of the figure represent close-up views of the atomic interactions between and (left); (center); and (right). (C) A view of AG7088, a Michael addition adduct, bound in the active site of HRV2-3C (57). The atom coloring for the inhibitot and enzyme is the same as that used in panel A. The hydrogen bonds between donor and acceptor atoms are represented by dashed lines. This inhibitor is covalently attached to the sulfur atom of Cysl47.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plateb 12 [chapter 17]

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Color Plateb 12 [chapter 17]

Comparison of the active sites of (A) PV1 3C, (B) HAV 3C, and (C) HRV2 3C. (A) A computer-generated model of residues to of Ala-Lys-Val-Gln- Gly-Pro (cleavage site between 3B and 3C of the polyprotein) in the active site of PV1-3C. The atomic color coding for the substrate is blue, nitrogen; orange, oxygen; and gray, carbon. For the enzyme, color coding is blue, nitrogen; red, oxygen; the residues forming subsites , , , , and are represented by different colors for the C atoms. Hydrogen bonds are designated by dashed lines between donor and acceptot atoms. Three close-ups of the subsites are shown below; and (left); (center); and (right). (B) A view of the computer-generated HAV-3C/substrate model. The color schemes are the same as those shown in panel A. The substrate was generated from the residues of the cleavage site between VPl and 2B of the HAV polyprotein (Leu-Phe-Ser-Gln-Ala-Lys). Hydrogen bonds are represented by dashed lines between donor and acceptor atoms. The three lower portions of the figure represent close-up views of the atomic interactions between and (left); (center); and (right). (C) A view of AG7088, a Michael addition adduct, bound in the active site of HRV2-3C (57). The atom coloring for the inhibitot and enzyme is the same as that used in panel A. The hydrogen bonds between donor and acceptor atoms are represented by dashed lines. This inhibitor is covalently attached to the sulfur atom of Cysl47.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 13 [chapter 17]

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Color Plate 13 [chapter 17]

RNA-binding sites on PV1-3C (left) and on HAV-3C (right). The segments of secondary sttuctute are colored as in Color Plate 11 . The backbone of the consetved sequence Lys-Phe-Arg-Asp-Ile is colored gray with the side chains teptesented (Lys and Arg, blue; Phe and He, green; Asp, red). The conserved segment is flanked by the two helices on the N and C termini of the molecules.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 14 [chapter 17]

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Color Plate 14 [chapter 17]

The structure of HRV2 2A. (A) A view of the HRV2-2A showing the secondary structural units (arrows for -strands, linking peptide segments as red tubing). The strands of the N-terminal domain are colored in cyan, those of the C-terminal domain are in lilac. The extensions to -strands bII and cII that contain the ditytosine loop are shown in gray. Helical turns are shown as green spiral ribbons. Residues in the active site Cys 106, His 18, and Asp35 are represented. The Zn binding site is also shown with the liganding residues Cys52, Cys54 and Cysll2, Hisl 114 on the back side of the molecule. The Zn is shown as a light blue sphere. The N and C tetmini are labeled N and C, respectively. (B) A stereodiagram showing the structural alignment of PV1-3C (red) and HRV2-2A (blue). The strands are labeled according to the topology of PV1 3C. Strand labels in the N-terminal domain have the roman numeral 1 appended; strand labels in the C-terminal domain have the roman numeral II appended. Secondary structural elements of PV1 3C that are missing in HRV2-2A are colored in gray.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 15 [chapter 17]

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Color Plate 15 [chapter 17]

The active site of HRV2 2A. (A) Stereodrawing showing the region around the active site of HRV2-2A. Carbon atoms are colored gray; nitrogen atoms, blue; and oxygen atoms, red. The sulfur of Cysl06 is colored yellow. Probable charge status of the residues is indicated. Hydrogen bonds between donor and acceptor atoms are represented by dashed lines. (B) Stereorepresentation of a model of an oligopeptide substrate (purple) occupying subsite to . The pentapeptide corresponds to the sequence of the polyprotein at the junction of VP1 and 2A (-Ile-Thr-Thr-Ala-Gly-). Hydrogen bonds between the substrate and HRV2-2A are represented by dashed lines. Reprinted from the (67) with permission of the publisher.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 16 [chapter 17]

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Color Plate 16 [chapter 17]

The structure of the FMDV L and its comparison to papain. (A) The structure of the Lb form of the FMDV L. View of the L complexed to six C-terminal residues of an adjacent molecule in the unit cell. Secondary structure elements in the N-terminal domain are colored blue, those in the C-terminal domain red. The C-terminal extension is colored brown. The acidic cluster of residues Aspl63, Aspl64, Glul65, and Aspl66 is shown in green. The dotted yellow region is expanded below to show the interactions of Lb (gray) involved in recognizing residues Leu200′ (P2) and Lys201′ (PI) (yellow ball and stick) of an adjacent molecule. (B) The structure of papain bound to leupeptin. Standard view of papain complexed to leupeptin. Secondary structure elements in the N-terminal domain of papain are colored blue, those in the C-terminal domain red. The tryptophan residue referred to in the text is indicated. The dotted yellow region is expanded below to show the interactions of papain (gray) involved in recognizing LeuI2 (P2) of leupeptin (yellow ball and stick). (C) The active site of Lb. Arrangement of amino acid side chains around the active site of Lb, as viewed down the central -helix. The catalytic tesidues of Lb Asn46, Cys51, Hisl48, and Aspl63 are shown. The acidic cluster (Aspl63-Aspl66) in the S′ binding region is also shown. The orientation of the amide group of Asn46 is maintained by a network of hydrogen-bond interactions (dotted lines) with the main-chain nitrogen of Asp49 and the side chains of Asn54 and Asp 164. (D) The active site of papain. Arrangement of amino acid side chains around the active site of papain, as viewed down the central -helix. The catalytic residues of papain Gln P-19, Cys P-25, His P-159, and Asn P-175 are shown. Hydrogen bonds are indicated. The residue Trp P-177, fully conserved in papain-like enzymes, which covers the hydrogen bond between essential catalytic tesidues Asn P-175 and His P-159, is also shown. The PDB coordinates used to make the drawings are 1QOL for the L (36) and 1POP for papain complexed with leupeptin (76), respectively. Parts (C) and (D) reprinted from the (36) with permission of the publisher. Color Plates 11 to 16 were drawn using the program MOLSCRIPT (50), with modifications by Esnouf (24) and Raster3D (61).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 17 [chapter 20]

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Color Plate 17 [chapter 20]

Confocal laser scanning micrographs. Each image area is 19 × 22 .m. (a–c) PV-infected cell, (a) Localization of plus-strand PV RNA and (b) of minus-strand PV RNA in the same cell, visualized by fluorescent in situ hybridization, (c) Overlay of (a) and (b), plus- and minus-strand RNA colocalize in distinct structures (yellow), (d–f) Formation of the PV replication complex in . (d) Vesicles induced by protein 2BC-Flag (red) and plus-strand RNA of superinfecting PV (green). PV does not use preformed vesicles for the formation of its replication complex, (e) Transfection of a nonreplicating construct (pE5PVΔP1), coding for the entire P2 and P3 region. The induced vesicles (red) and the nonreplicating RNA (green) are found in separate structures and do not form a replication complex, (f) Transfection of a replicon, coding for the entire P2 and P3 region. The induced vesicles (green) and the replicating RNA (red) form replication complexes (yellow), (d–f) Reprinted from (32), with permission.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 18 [chapter 21]

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Color Plate 18 [chapter 21]

Comparison of poliovirus 3D 1 to human immunodeficiency virus reverse transcriptase (HIV RT) and hepatitis C virus (HCV) NS5B. Crystal structure of (A) 3D (35), (B) HCV NS5B (15, 53), and (C) HIV-1 RT (39). The molecules are colored in gray. Sttuctural motif designations ate according to Hansen et al. (35). Conserved structural motifs common to all three molecules are colored as follows: motif A, red; motif B, green; motif C, yellow; motif D, blue, motif E, purple; motif F, black. Images were rendered using MOLSCRIPT (49) and Rastet3D (58). (D) Model of 3D (complete) based upon sequence and structural homology to NS5B. Regions missing from the poliovirus crystal structure were reconstructed by superpositioning the two structures and replacing the missing regions from the 3D structure with the corresponding region from NS5B. The amino acid side chains were changed to those of 3D using the program O (44). Images were rendered using the program WebLab Viewer (Molecular Simulations, Inc.).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 19 [chapter 21]

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Color Plate 19 [chapter 21]

Electrostatic potential diagrams 3D (A) Electrostatic potential diagram of the molecular surface of 3D. Electrostatic surface potentials were calculated for the complete 3D odel using the program GRASP (63). The orientation in panel A has been rotated by 180° about the vertical axis of Color Plate 18D . Regions in blue are positively charged, and those in red are negative charged. The location of the fingers, palm, and thumb subdomains are noted. Basic residues lining are proposed NTP/PP channel are labeled. Residues in these positions are predicted to make contact with nucleotides entering the active site, nucleotide in the NTP-binding site, and/or pyrophosphate. (B) Electrostatic potential diagram of the RNA-binding groove. The image is rotated by 90° about the horizontal axis of the page relative to the image shown in (A). Lys-61 has been labeled for referance. The palm subdomain is behind the molecule and cannot be seen from this view. The region in which the fingers and thumb subdomain make contact in labeled Finger Tips. The fingers subdomain is subdivided into the regions by a groove (labeled RNA Binding Groove) that may be important for nucleic acid binding based on modeling studies (Gohare and Cameron, unpublished). the RNA-binding groove is predicted to make contact with template RNA leading into the active site of the polymerase, which, in turn, may increase the stability of the enzyme on nucleic acid.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 20 [chapter 21]

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Color Plate 20 [chapter 21]

Unit cell of poliovirus 3D. (A) The unit cell of 3D crystals based on the original structure. The unit cell is composed of two asymmetric units, each containing two molecules (one shown in red, the other shown in blue). Interfaces I and II are labeled. Interface I forms via the back of the palm of one molecule (red) and the back of the thumb of the other (blue). Interface II corresponds to the back of the fingers of one molecule (red) and the top of the thumb of the other (blue). In this image, interface II is predicted to be stabilized by intermolecular contacts of the amino terminus of one molecule (red) extending across interface II to the other (blue). (B) The unit cell of 3D based on the complete model. Interfaces I and II form via similar interactions as those described in panel A. However, based on observations made in the NS5B structure, the amino terminus of each molecule makes intramolecular contacts with the thumb. Residues comprising interface II are the same in both panels A and B; however, the contribution of the amino terminus is different.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 21 [chapter 21]

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Color Plate 21 [chapter 21]

Fiber formation by 3D. Orientation of molecules involved in fiber formation occurs in a head-to-tail fashion along interface I as observed in the original crystal structure of 3D. The unit cell is shown (black box). The two principal axes perpendicular to the view axis are labeled. (A) View down the -axis. Each fiber shown represents a single plane (1 to 3) of fibers each stacked one on top of the other. For clarity only one fiber from each plane is shown, with the center of the plane located within the unit cell (black box). For example, the plane of the purple fiber could be constructed by translating the fiber in increments of one unit cell dimension along the -axis in both directions. Each fiber is related to the others by rotation of 120° about the -axis (axis perpendicular to the plane of the page) and 180° about the central axis of each fiber. (B) View down the -axis. The image shown in panel A has been rotated by 90° about the vertical axis of the page. Planes 1 to 3 can be observed in this view. The fiber in plane 2 (purple) lies along the principal axis of this view (-axis). In this orientation, each plane is approximately one-third the thickness of the unit cell in the -direction. The molecules in each plane make contact with molecules in the adjacent plane via interface II.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 22 [chapter 21]

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Color Plate 22 [chapter 21]

Interfaces I and II. Atoms of the amino acid side chains are color coded as follows: gray, carbon; blue, nitrogen; red, oxygen. (A) Close-up view of the top of interface I. Amino acids involved in specific interactions are shown. Leu-446 on the back of the thumb of one molecule (blue) extends into a hydrophobic pocket found on the back of the palm of the other molecule (red). (B) The bottom of interface I is shown. Arg-455 hydrogen bonds to Asp-349; Arg-456 hydrogen bonds to both Asp-339 and Ser-341. The carboxyl tetminus is 5 amino acids from Arg-456. (C) Interface II based on the original description by Hansen et al. (35). The amino terminus of the molecule in red extends across the junction between the two molecules and makes specific contacts with the top of the thumb of the molecule in blue. Val-33 and Phe-30 rest in a hydrophobic pocket formed by Ile-401, Ile-436, and VaI-439. (D) Interface II based on the complete model for 3D. Amino acid side chains shown in (C) are also involved in similar interactions but have not been relabeled. The amino-terminal strand shown in red in (C) is predicted to originate from the same molecule (i.e., the blue molecule) as observed in the complete model. Additional interactions that may stabilize interface II are predicted based on both the original structure and the complete model. Asp-79 hydrogen bonds with Arg-443. Arg-443 is located on the top of the thumb in a region that consists, in part, of a basic patch. Asp-89 (red molecule) and Glu-26 (blue molecule) may be important for stabilization of interface II by serving as ligands (dashed lines) for divalent cations such as Zn (shown here as Ca based on the original 3D crystal strucrure).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 23 [chapter 21]

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Color Plate 23 [chapter 21]

Model of a 3Dr-primer/template-nucleotide complex. (A) The ternary complex. Primer, template, and nucleotide are color coded as follows: primer, yellow; template, blue; nucleotide, magenta. Metal ions involved in catalysis are depicted as gray spheres. Amino acid side chains are color coded as in Color Plate 20 . (B) Interaction of metal ions required for catalysis. Metal ions (labeled A and B) are coordinated by the triphosphate moiety of the incoming nucleotide (dashed lines), as well as by amino acid side chains of 3D. Asp-233 (motif A) and Asp-328 (motif C) are strictly conserved among all nucleic acid polymerases. Asp-233, Asp-328, and the 3′-OH and oxygen atoms on the -phosphate coordinate the metal ion at position A. The 3′-OH attacks the -phosphorus (depicted as an arrow) of the incoming nucleotide. Metal ion B is required for stabilization of the triphosphate moiety of the incoming nucleotide and is coordinated by oxygen atoms at the -, -, and -positions of the triphosphate moiety as well as by Asp-233 and the carbonyl oxygen of Tyr-234. An oxygen on the -phosphate hydrogen bonds to the 3′-OH as well as the backbone amide of Tyr-237. The oxygen on the -phosphate hydrogen bonds to the backbone amide of Gly-236. (C) Residues involved in selection of the 2′-OH are shown. Asp-238 is shown hydrogen bonding (black lines) to the 2′-OH of the incoming nucleotide as well as to Thr-293 and the backbone amide of Ser-288. Asn-297 hydrogen bonds to the 2′-OH of the incoming nucleotide as well. The 3′-OH, not labeled here for clarity, hydrogen bonds to the backbone amide of Asp-238 and an oxygen atom on the -phosphate of the triphosphate moiety. (D) Role of the conserved glycine in the Gly-Asp-Asp motif (motif C). A surface contour of structural motif C is shown. The incoming nucleotide (magenta) and the penultimate primer nucleotide (yellow, P-2) are shown as sticks. The nucleotide on the 3′ end of the primer is shown as a surface contour (yellow). The 2′-OH of the nucleotide at the 3′ end of primer is labeled (arrow). Based on superpositioning with the HIV-1 ternary complex structure (32, 39), it is possible that a side chain larger than glycine (methionine in the case of HIV-1 RT, shown as a blue surface) will clash with the 2′-OH at the 3′ end of primer. The presence of a glycine (as part of the Gly-Asp-Asp motif) may be required to accommodate the 2′-OH on the primer strand.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 24 [chapter 21]

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Color Plate 24 [chapter 21]

Structure-based sequence alignment of 3D, NS5B, and HIV RT. The complete sequence of 3D is shown based on a structural alignment with NS5B and HIV-1 RT. The sequence of NS5B is shown up to residue 480. Only the sequences of stmctural elements of HIV-1 RT common to 3D and NS5B ate shown. Numbers at the end of lines correspond to the last amino acid in that row. For clarity, the corresponding numbers have been omitted for HIV-1 RT. Secondary structures are indicated based on those obsetved in the complete structure of NS5B and are shown as blue arrows (-sheets) or red boxes (-helices). Secondary stmctures are labeled according to theit designation in the otiginal 3D structure; unlabeled boxes correspond to regions not present in the 3D structure. Residues in white are conserved; those in yellow are conservative substitutions between the molecules. Conserved structural motifs A to F are surrounded by open black boxes. Regions predicted to make contact with nucleic acid and/or nucleotide are boxed and color coded as noted at the bottom of the figure (adapted with permission from Bressanelli et al. [15]).

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 25 [chapter 29]

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Color Plate 25 [chapter 29]

Comparative neuropathology of poliovirus infection. CD155 tg mice (B) or wild-type mice (C) were infected with poliovirus by the intracerebral route. Rectangles within whole mount sections (left panels) indicate the localization of inserts shown at higher magnification (right panels). (A) Horizontal sections through the spinal cord of uninfected CD155 tg mice depict groups of large, dark-staining cells resident within the anterior horns (motor neurons). (B) Poliovirus infection selectively affects anterior horn motor neurons, which, as a result of lytic infection, are destroyed. The extraordinarly specific nature of the neuropathology of poliomyelitis can be observed at higher magnification, where the remnants of former motor neurons (“ghosts”) are indicated by arrowheads. Remarkably, no other cellular compartment within the CNS shows any signs of damage. (C) Experimental infection of wild-type mice will elicit neurological symptoms only after intracerebral inoculation of poliovirus. In the absence of the human poliovirus receptor CD155, disseminated lesions affecting the entire CNS indiscriminately can be observed. Dense lymphocytic infiltrates ate seen throughout the white and gray matter, and extensive tissue destruction with no discernible specificity results in the formation of a large necrotic area within the right anterior horn. The insert shown depicts intact motor neurons (arrowheads) within the spinal cord anterior horn surrounded by numerous infiltrative lesions. Luxol-fast blue, periodic acid-Schiff, hematoxylin stain; whole mount sections are shown at 4×, inserts at 12× magnification.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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Image of Color Plate 26 [chapter 29]

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Color Plate 26 [chapter 29]

(1) Activity of the CD155 promotet in the developing CNS. A–D. Transcephalic horizontal sections through mouse embryos transgenic for -galactosidase under control of the CD155 promoter reveal cell-specific activity. The location of sections taken is indicated around the whole mount embryo in the center. CD155 promoter activity extends throughout the entire floor plate (fp) stretching from the caudal diencephalon (di; A) and the mesencephalon (me; A) into the medullary raphe (mr; B) and the spinal cord (C, D). Staining was also observed in the future optic chiasm (oc; B), the notochord (nc; C), and the spinal cord anterior horn proper (ah; C). (II) A schematic diagram of the morphogenesis of the anterior spinal cord depicts the sequence of events leading to motor neuron differentiation (A–D). Indentation of the neural plate (A) produces the neural fold (B), which, upon closure, forms the primitive neural tube (C) and spinal cord (D). The anterior commissure of the neural tube is formed by floor plate cells, which develop upon inductive signals emanating from the notochord. Floor plate cells proper are the source for inductive signals that induce motor neuron (mn) differentiation in the adjacent spinal cord anterior horn (D). The induction, differentiation, and maturation of motor neurons are critically influenced by the signaling molecule sonic hedgehog (the action of sonic hedgehog is indicated by arrows and arrowheads). X-Gal stain for -galactosidase with eosin counterstain (32); whole mount embryo is shown at 3.2×, sections at 16× magnification.

Citation: Semler B, Wimmer E. 2002. Color Plates, In Molecular Biology of Picornavirus. ASM Press, Washington, DC.
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