Ribbon representation

Fig. 4.1.13 A ribbon representation of the crystal structure of recombinant acquorin molecule showing the secondary structure elements in the protein. Alpha-helices are denoted in cyan, beta-sheet in yellow, loops in magenta coelenterazine (yellow) and the side chain of tyrosine 184 are shown as stick representations. From Head et al., 2000, with permission from Macmillan Publishers.

FIGURE 1119 The lysozyme molecule is a typical enzyme molecule. Lysozyme is present in a number of places in the body, including tears and the mucus in the nose. One of its functions is to attack the cell walls of bacteria and destroy them. This "ribbon" representation shows only the general arrangement of the atoms to emphasize the overall shape of the molecule the ribbon actually consists of amino acids linked together (Section 19.13). 

Fig. 1. Ribbon representation of the three-dimensional structure of D. gigas hydro-genase (32). The large subunit is represented in dark gray. Fe is represented by black spheres, Ni by gray spheres, and inorganic sulfur by white spheres. The C-terminal end of the large subunit is close to the Ni smd completely buried in the structure.

PI. 3.1 A MUP peptide backbone ribbon representation, shown in two orthogonal projections (left p-sheet framework right binding-cavity, highlighted) (from Luckc et at., 1999). 

Figure 18 Structural model for A0 (1-40) protofilaments, derived by energy minimization with constraints based on solid-state NMR data, (a) Ribbon representation of residues 8-40, viewed down the long axis of the protofilament, (b) Atomic representation of residues 1-40. From Ref. 141.

Figure 5.4 (a) Stereo ribbon representation of hFBP with Fe3+ ligands shown. 6-sheets are gold, a-helices are cyan, and other structures are dark blue, (b) N-lobe of lactotransferrin. Secondary structure elements are coloured as in hFBP, except for grey regions, which are those most different from hFBP. From Bruns et al., 1997. Reproduced by permission of Nature Publishing Group. 

Figure 2.5 Ball-and-stick and ribbon representations of an a-helix. Reproduced from Sun, P. and Boyington. 1997. Current Protocob in Protein Science by kind permission of the publisher, John Wiley and Sons...

Fig. 12.4 The results of the determination of the rotational diffusion tensor of the /7ARK PH domain A fit of the orientational dependence of the experimental values ofp for the /iARK PH domain and B a ribbon representation of the 3D structure of the protein, with the orientation of the diffusion axis indicated by a rod. Shown in A are the experimental (symbols) and the best fit (line) values ofp (Eq.

Figure 21 Structure of the collagen X NCI trimer (PDB accession number 1GR3). Ribbon representation of the NCI trimer viewed down the crystallographic three-fold axis Is given. Ca + Ions are represented as pink spheres. The figure was generated using the UCSF Chimera package.

Figure 10 N M R structural analysis of carrier domains. Three conformations of the PCP domain from tyrocidine synthetase (brown box) and the NMR structure of the related AGP domain from a polyketide synthase. The star symbol signifies the position of the conserved phosphopantetheinylated serine residue. The protein ribbon representations are rainbow colored from red (N-terminus) to violet. PDB codes A/H state, 2GDW H-state, 2GDX A-state, 2GDY AGP, 2AF8.

Fig. 5 The crystal structure of the antibody-octapeptide complex, with STD-NMR intensities mapped onto the bound peptide. Residues of the antibody combining site are shown in purple, with selected residues labeled, and the direction of the backbone indicated in ribbon representation. Residues of the peptide are labeled in italics. Heavy atoms of the peptide are shown in gray, while the default color for hydrogen atoms is white. Observed STD-NMR intensities are mapped onto hydrogen atoms of the peptide by color, with red indicating 50-100% enhancement, orange 30-50% enhancement, a.nd yellow < 30% enhancement. Protons that are definitely not enhanced are shown in black those for which no enhancement could be determined (due to interference by other resonances, or not observable in the ID spectrum) remain white. Reproduced with permission from [100]. 2004 Elsevier Science...

Fig. 1. The core particle, the DNA superhelix and H2B and H3 N-terminal tails, (a) Space-filling representation of the 2.8 A crystal structure of the 146 bp human a-satellite nucleosome core particle [22]. The dyad is in the plane of the paper and the superhelix axis slightly off that plane. Positive and negative numbers mark the superhelix locations (SHL) in the upper and lower gyres, respectively, and the dotted curve follows the path of the double helix axis, (b) Ribbon representation of the DNA superhelix slit along a line parallel to its axis, opened out and laid flat on the paper surface. SHL are also indicated, together with H2B and H3 tails passage points between the gyres. (From Fig. 5 in Ref [29].)...

Figure 2.1 Structures of histone acetyltransferases (HATs). Ribbon representation of the structures of the HAT domains of (a) Tetrahymena thermophila CcnS (PDBcode Iqsr), (b) Saccharomyces cerevisiae Hatl (PDB code Ibob), (c) S. cerevisiae Esal (PDB code Imja),...

Figure 2.2 Structures of CcnS histone acetyltransferase (HAT) bound to coenzymeA and various peptides. Schematic representation of Tetrahymena thermophiia CcnS HAT domain (ribbon representation) bound to coenzymeA and 19mers (both shown as ball and sticks) from (a) histone H3 (PDB code lpu9),...

Figure 2.3 Structures of mammalian classic histone deacetylases. Ribbon representation of the conserved catalytic domain of (a) class I human HDAC8 in complex with trichostatin A (TSA PDB code lt64), (b) human HDAC8 Tyr306Phe inactive mutant in complex with a peptidic acetyl-lysine substrate (PDB code 2v5w), (c) class I la human...

Figure 2.4 Structures of histone deacetylases from the sirtuin family. Ribbon representation of the structures of the conserved catalytic domain of histone deacetylases (a) Homo sapiens SirT2 (PDB code IjSf) and (b) Thermotoga maritima Sir2 bound to NAD and an acetylated p53 peptide (PDB code 2h4f).

PAD4 is a Ca -dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. (a) Ribbon representation of the PAD4/benzoyl-L-arginine amide complex (PDB code Iwda) in the presence of the ions (green spheres). 

Figure 2.10 Structures of mammalian DNA methylases. (a) Ribbon representation of the structure of the tetrameric complex formed between the C-terminal domain of Dnmt3a2 (orange) and the C-terminal domain of Dnmt3L (green) (PDB code 2qrv). The AdoHcy molecules are colored cyan.

Fig. 13. Structural dynamics of TAR RNA in response to increasing Mg2+ concentrations. (A) The TAR inter-helical conformation as a function of [Mg] [TAR] stoichiometry. Ribbon representation of the relative orientation of stem I (bottom) and II (top) determined by superimposing stem-specific principal axes. The helix axis of stem II is superimposed for all three conformations along the molecular z direction. (B) The generalized degree of order ( ) for stem I (lower line) and II (upper line), as a function of [Mg] [TAR] stoichiometry. Addition of Mg2+ leads to attenuations in the difference between helix-specific values indicating quenching of inter-helical motions.

Shown here are cytochrome c (PDB ID 1CCR), lysozyme (PDB ID 3LYM), and ribonuclease (PDB ID 3RN3). Each protein is shown in surface contour and in a ribbon representation, in the same orientation. In the ribbon depictions, regions in the f) conformation are... 

An outstanding summary of protein structural patterns and principles the author originated the very useful ribbon representations of protein structure. 

FIGURE 11-43 Structure of the lactose transporter (lactose permease) of E. coli. (a) Ribbon representation viewed parallel to the plane of the membrane shows the 12 transmembrane helices arranged in two nearly symmetrical domains shown in different shades of blue. In the form of the protein for which the crystal structure was determined, the substrate sugar (red) is bound near the middle of the membrane where it is exposed to the cytoplasm (derived from PDB ID 1 PV7). (b) The structural changes postulated to take place during one transport... 

Figure 5-39 (A) Stereoscopic ribbon representation of the E. coli methionine repressor-operator complex. Two subunits form a dimer with a double-stranded antiparallel 3 ribbon that fits into the major groove of the DNA in the B form. One strand is shaded more darkly than the other.

Figure 7-12 A ribbon representation of the ornithine decarboxylase dodecamer. Six dimers of the 730-residue subunits are related by C6 crystallographic symmetry. MolScript drawing from Momany et al.66 Courtesy of Marvin Hackert.

Figure 8-21 Views of the tetrameric K+ channel from Streptococcus lividans. (A) Ribbon representation as an integral membrane protein. Aromatic amino acids on the membrane-facing surface are also shown. (B) Stereoscopic view. (C) Stereoscopic view perpendicular to that in (B) with a K+ ion in the center. From Doyle et al.366...

Figure 19-15 Ribbon representation of chicken skeletal myosin subfragment-1 showing the major domains and tryptic fragments. Prepared with the program MolScript. From Rayment.157...

Figure 31-6 Three-dimensional ribbon representation of the structure of a complex of a soluble Fc fragment of a human IgGl molecule. Pro 329 of the IgG and Trp 87 and Trp 110 of the Fc-receptor fragment form a "proline sandwich/ which is shown in ball-and-stick form. The oligosaccharide attached to the Fc fragment of the antibody and the disulfide bridge between the two Cys 229 residues (at the N termini of the C2 domains of the heavy y chains) are also shown. The small spheres on the Fc receptor fragment are potential sites for N-glycosylation. From Sondermann et al.107 Courtesy of Uwe Jacob.

Fig. 14. Stereo ribbon representation [76] of the FucA subunit architecture showing the central nine-stranded -pleated sheet. The active site zinc ion is marked by a black circle...

Fig. 18. Stereo ribbon representation [76] of the transketolase dimer from Saccaromyces cerevisiae...

Fig. 2. Structures of family A, B, X, Y, and RT polymerases. The proteins are in ribbon representation. The fingers, palm, and thumb subdomains are color-coded in gold, red, and green, respectively. (A) Structure of apo Klentaql (family A). The 3 -5 vestigial exonuclease domain is indicated in silver. (B) Structure of apo RB69 DNA polymerase (family B). The 3 -5 exonuclease domain and the N-terminal domain are indicated in grey and silver, respectively. (C) Structure of apo pol / DNA polymerase (family X). The lyase domain is indicated grey. (D) Structure of the Dpo4 DNA polymerase (family Y). The litde finger subdomain is indicated in silver. (E) Structure of the p66 subunit of reverse transcriptase (RT family). The RNAseH and connection subdomains are indicated in grey and silver, respectively.

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