Ribbon drawing

FIGURE 6.7 The three-dimensional structures of two proteins that contain substantial amounts of rx-helix in their structures. The helices are represented by the regularly coiled sections of the ribbon drawings. Myohemery-thrin is the oxygen-carrying protein in certain invertebrates, including Sipunculids, a phylum of marine worm. (Jane Richardson)... 

Superposition of residues 83 to 248 of the family of structures is shown in Figure 9 viewed along the long axis of the catalytic helix. Residues 249 to 255 are disordered and therefore are not shown. In Figure 10 ribbon drawings of two views of the molecule are shown, one from above the (3-sheet and the other from below the Si subsite. The secondary structure of sfSTR consists of a five stranded [. -sheet with four parallel strands and... 

The problem of validation has been of long-term interest to the author. Ribbons (Carson, 1997) was presented as a visual sanity check of a structure, mapping properties of crystallographic interest to the ribbon drawing (Carson and Bugg, 1988). Residues were colour-coded by main-chain and... 

Fig. 3. (a) Copper site in plastocyanin. (b) Ribbon drawing of the plastocyanin backbone, (c and d) Schematic of plastocyanin topology. 

Fig. 7. (a) Ribbon drawing of immunoglobulin domain, (b and c) Schematic of the folding topology of the immunoglobulin domain. 

In the third chapter, Elinor T. Adman presents a comprehensive view of the structures of copper-containing proteins. This view includes the topological folding of many of these proteins, as shown by ribbon drawings, as well as details of copper-ligand interactions. 

Figure 2-14 A "ribbon" drawing of the 307- residue proteinhydrolyzing enzyme carboxypeptidase A. In this type of drawing wide ribbons are used to show 3 strands and helical turns while narrower ribbons are used for bends and loops of the peptide chains. The direction from the N terminus to C terminus is indicated by the arrowheads on the 3 strands. No individual atoms are shown and side chains are omitted. Courtesy of Jane Richardson.117...

From Guss and Freeman.116 (B) Ribbon drawing of immunoglobulin fold. This is a common structure in domains of the immunoglobulins and in many other extracellular proteins. Two layers of antiparallel (3 sheet are stacked face to face to form a flattened barrel. One disulfide bridge is always present and is represented as a thick rod. From J. Richardson.117 (C) Five tandem fibronectin type III domains. 

Figure 2-21 (A) Ribbon drawing of the transcription factor called Max in a complex with DNA. The C termini of the peptide chains are at the top.169 Courtesy of S. K. Burley.

Figure 2-22 Ribbon drawing of an up-and-down four-helix bundle in myohemerythrin. The two spheres represent the two iron atoms which carry an 02 molecule. They are coordinated by histidine and aspartate side chains. Courtesy of J. Richardson.117...

Figure 2-28 The eight-fold oc/(3 barrel structure of triose phosphate isomerase. From Richardson. (A) Stereoscopic view. (B) Ribbon drawing. Courtesy of Jane Richardson.117...

Figure 7-8 (A) Electron micrograph of the rod-shaped particles of tobacco mosaic virus. Omikron, Photo Researchers. See also Butler and Klug.42 (B) A stereoscopic computer graphics image of a segment of the 300 nm long tobacco mosaic virus. The diameter of the rod is 18 nm, the pitch of the helix is 2.3 nm, and there are 16 1 3 subunits per turn. The coat is formed from 2140 identical 17.5-kDa subunits. The 6395-nucleotide genomic RNA is represented by the dark chain exposed at the top of the segment. The resolution is 0.4 nm. From Namba, Caspar, and Stubbs.47 (C) A MolScript ribbon drawing of two stacked subunits. From Wang and Stubbs.46...

Figure 7-10 (A) Model of the F-actin helix composed of eight monomeric subunits. The model was constructed from the known structure of the actin monomer with bound ADP using X-ray data from oriented gels of fibrous actin to deduce the helical arrangement of subunits. The main interactions appear to be along the two-start helix. See also Holmes ef a/.62 (B) Ribbon drawing of an actin monomer with the four domains labeled. Courtesy of Ivan Rayment.

Figure 7-13 (A) MolScript ribbon drawing of a subunit of the iron oxide storage proteins L-ferritin from amphibian red cells. This 4-helix bundle is represented by cylinders of 1.3 nm diameter in the oligomer.

Figure 7-18 Stereoscopic MolScript ribbon drawings of the B chains (A chains omitted) of (A) hexameric 2-zinc pig insulin. (B) A phenol complex of the same protein. Within each dimer the B chains are shaded differently. The Zn2+ ions are represented by white spheres and the coordinating histidine side chains are shown. Six noncovalently bound phenol molecules can be seen, as can several conformational differences. From Whittingham et al.B7 Courtesy of Peter C. E. Moody.

Figure 7-20 (A) Subunit assembly of two C3 catalytic trimers (green) and three R2 regulatory dimers around the periphery in aspartate carbamoyltransferase. After Krause et a/.109 Courtesy of William N. Lipscomb. The aspartate-and carbamoylphosphate-binding domains of the catalytic subunits are labeled Asp and CP, respectivley, while the zinc and allosteric domains of the regulatory subunits are labeled Alio and Zn, respectively. (B) Ribbon drawing of a single pair of regulatory (left) and catalytic (right) subunits with the structural domains labeled. MolScript drawing from Thomas et al.no...

Figure 8-20 MolScript ribbon drawings of the OmpF porin of E. coli. (A) View of the 340-residue monomer. (B) View of the trimer looking down the threefold axis. From Wa-tanabe et al3is From atomic coordinates of Cowan et al.3i9 (C) Molecular model of the constriction zone of the PhoE porin. Locations of key residues are shown, with positions of homologous residues in OmpF given in parentheses. Extracellular loops have been omitted. Constructed from coordinates of Cowan et al.349 by Samartzidou and Del-cour.342 Courtesy of Anne Delcour.

Figure 8-24 (A) MolScript ribbon drawing of the periplasmic histidine-binding protein HisJ, a component of an ABC transporter system of Salmonella. The bound L-histidine is shown as a ball-and-stick model. (B) Stereoscopic view of the histidinebinding site showing hydrogen-bonding interactions of protein side chains with the histidine. From Oh et al.i60 Courtesy of Giovanna Ferro-Luzzi Ames.

The three-dimensional structure of cholera toxin.6 Side view of the p subunit pentamer as a ribbon drawing. Bound noncovalently to it are five molecules of the ganglioside Gm1 (compare with the structure in Fig. 7-5). The diacyl glycerol parts of the gangliosides are buried in the membrane that lies below the toxin molecule. Courtesy ofW.G.J. Hoi. 

Figure 11-14 Ribbon drawing of the three-dimensional structure of adapter protein Grb2. The two SH3 domains at the N and C termini are labeled, as is the central SH2 domain. Produced with programs MolScript and Raster3D. From Maignan et al.i76 Courtesy of Amaud Ducruix.

Figure 16-3 Structure of the protein shell of ferritin (apoferritin). (A) Ribbon drawing of the 163-residue monomer. From Crichton.62 (B) Stereo drawing of a hexamer composed of three dimers. (C) A tetrad of four subunits drawn as a space-filling diagram and viewed down the four-fold axis from the exterior of the molecule. (D) A half molecule composed of 12 subunits inscribed within a truncated rhombic dodecahedron. B-D from Bourne et al.7i...

Figure 16-31 (A) Structure of molybdopterin cytosine dinucleotide complexed with an atom of molybdenum. (B) Stereoscopic ribbon drawing of the structure of one subunit of the xanthine oxidase-related aldehyde oxidoreductase from Desulfo-vibrio gigas. Each 907-residue subunit of the homodimeric protein contains two Fe2S2 clusters visible at the top and the molybdenum-molybdopterin coenzyme buried in the center. (C) Alpha-carbon plot of portions of the protein surrounding the molybdenum-molybdopterin cytosine dinucleotide and (at the top) the two plant-ferredoxin-like Fe2S2 clusters. Each of these is held by a separate structural domain of the protein. Two additional domains bind the molybdopterin coenzyme and there is also an intermediate connecting domain. In xanthine oxidase the latter presumably has the FAD binding site which is lacking in the D. gigas enzyme. From Romao et al.633 Courtesy of R. Huber.

Figure 18-10 Structure of mitochondrial cytochrome c oxidase. (A) Stereoscopic Ca backbone trace for one monomeric complex of the core subunits I, II, and III. (B) Stereoscopic view showing all 13 subunits. The complete complex is a dimer of this structure. From Tsukihara et al.125 (C) MolScript ribbon drawing of one monomeric unit. The horizontal lines are drawn at distances of + 1.0 and +2.0 nm from the center of the membrane bilayer as estimated from eight phospholipid molecules bound in the structure. From Wallin et al.127 Courtesy of Arne Elofsson.

Figure 19-9 Stereoscopic ribbon drawing of the proposed structure of a thin actin filament with tropomyosin coiled-coils bound on opposing sides.124 Five actin nomomers are assembled in the structure as is also illustrated in Fig. 7-10. From Lorenz et al.125 Courtesy of Michael Lorenz.

Figure 19-17 Ribbon drawing of human kinesin with bound Mg ADP. From Gulick rf a/.174 Courtesy of Ivan Rayment and Andy Gulick.

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