Ribbon diagrams

Figure 12.7 Ribbon diagram of one subunit of potin from Rhodobacter capsulatus viewed from witbin tbe plane of tbe membrane. Sixteen p strands form an antiparallel p barrel tbat traverses tbe membrane. Tbe loops at tbe top of tbe picture are extracellular whereas tbe short turns at tbe bottom face the periplasm. The long loop between p strands 5 and 6 (red) constricts the channel of the barrel. Two calcium atoms are shown as orange circles. (Adapted from S.W. Cowan, Curr. Opin. Struct. Biol. 3 501-507, 1993.)...

Figure 12.18 Ribbon diagram showing the a (red) and the P (blue) chains of the light-harvesting complex LH2. Each chain forms one transmembrane a helix, which contains a histidine residue that binds to the Mg atom of one bacteriochlorophyll molecule. (Adapted from G. McDermott et al.. Nature 374 517-521, 1995.)...

Figure 13.19 Ribbon diagram of the stmcture of the extracellular domain of the human growth hormone. The hormone-binding region is formed by loops (yellow) at the hinge region between two fibronectin type III domains. (Adapted from J. Wells et al., Annu. Rev.

Figure 13.20 Ribbon diagram of the structure of a 1 2 complex between the human growth hormone and the extracellular domains of two receptor molecules. The two receptor molecules (blue) bind the hormone (red) with essentially the same loop regions (yellow).

Figure 13.30 Ribbon diagram of the structure of Src tyrosine kinase. The structure is divided in three units starting from the N-terminus an SH3 domain (green), an SH2 domain (blue), and a tyrosine kinase (orange) that is divided into two domains and has the same fold as the cyclin dependent kinase described in Chapter 6 (see Figure 6.16a). The linker region (red) between SH2 and the kinase is bound to SH3 in a polyproline helical conformation. A tyrosine residue in the carboxy tail of the kinase is phosphorylated and bound to SH2 in its phosphotyrosine-binding site. A disordered part of the activation segment in the kinase is dashed. (Adapted from W. Xu et al.. Nature 385 595-602, 1997.)...

Figure 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

Figure 14.7 Ribbon diagram of one subunit of the globular form of transthyretin. The p strands are labeled A to H from the amino end. Strands C and D are thought to be unfolded to produce the conformation that forms amyloid fibrils. (Adapted from C.C.F. Blake et al., /. Mol. Biol. 121 339-356, 1978.)...

Figure 15.22 T-cell receptor stucture shown as a ribbon diagram. The anbgen-binding site is formed by CDR loops (labeled 1 to 3) from the Va and Vp domain, as for antibodies.

Figure 15.24 Ribbon diagram (a) and topology diagram (b) of the fibronectin type III domain, which is composed of a three-stranded and a four-stranded p sheet packed together as a compressed barrel.

Figure 17.12 Ribbon diagram of EMPl bound to the extracellular domain of the erythropoietin receptor (EBP). Binding of EMPl causes dimerization of erythropoietin receptor. The x-ray crystal structure of the EMPl-EBP complex shows a nearly symmetrical dimer complex in which both peptide monomers interact with both copies of EBP. Recognition between the EMPl peptides and EBP utilizes more than 60% of the EMPl surface and four of six loops in the erythropoietin-binding pocket of EBP.

Figure 17.16 Ribbon diagram representations of the structures of domain B1 from protein G (blue) and the dimer of Rop (red). The fold of B1 has been converted to an a-helical protein like Rop by changing 50% of its amino acids sequence. (Adapted from S. Dalai et al.,...

FIGURE 17.30 (a) A ribbon diagram and (b) a molecular graphic showing two slightly different views of the structure of troponin C. Note the long a-helical domain connecting the N-terminal and C-terminal lobes of the molecule. 

FIGURE 22.18 Model of the R. viridis reaction center, (a, b) Two views of the ribbon diagram of the reaction center. Mand L subunits appear in purple and blue, respectively. Cytochrome subunit is brown H subunit is green. These proteins provide a scaffold upon which the prosthetic groups of the reaction center are situated for effective photosynthedc electron transfer. Panel (c) shows the spatial relationship between the various prosthetic groups (4 hemes, P870, 2 BChl, 2 BPheo, 2 quinones, and the Fe atom) in the same view as in (b), but with protein chains deleted. 

Fig. 1 A ribbon diagram of the crystal structure of a substrate complex of the homo-dimer HIV-1 protease (lkj7) (Prabu-Jeyabalan et al. 2002), Each monomer is shown in cyan and pink the substrate is shown in green, and the catalytic aspartic acids are highlighted in yellow...

Fig. 3 A ribbon diagram of the HCV NS3/4A protease ICU1 (Yao et al, 1999). The serine protease domain is shown in cyan with the catalytic triad highlighted in yellow, and the helicase domain is...

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

Fig. 2. The structure of the Fe protein (Av2) from Azotobacter vinelandii, after Geor-giadis et al. (1). The dimeric polypeptide is depicted by a ribbon diagram and the Fe4S4 cluster and ADP by space-filling models (MOLSCRIPT (196)). The Fe4S4 cluster is at the top of the molecule, bound equally to the two identical subunits, Emd the ADP molecule spans the interface between the subunits with MoO apparently binding in place of the terminal phosphate of ATP.

Fig. 3. The tetrameric structure of the MoFe protein (Kpl) from Klebsiella pneumoniae (7). The two FeMoco clusters and the P clusters are depicted by space-filling models and the polypeptides by ribbons diagrams (MOLSCRIPT (196)). The FeMoco clusters are bound only to the a subunits, whereas the P clusters span the interface of the a and j8 subunits.

Fig. 10. The putative transition-state complex formed between the Fe protein MgADP AlFj and the MoFe protein. For simplicity only one a/3 pair of subunits of the MoFe protein is shown. The polypeptides are indicated by ribbon diagrams and the metal-sulfur clusters and MgADP AlFi" by space-filling models (MOLSCRIPT (196)). The figure indicates the spatial relationship between the metal-sulfur clusters of the two proteins in the complex.

Figure 10 Ribbon diagrams of a single conformer of inhibited sfSTR from residues 83 to 250. (A) The complex is viewed from above the (1-sheet. The positions of the two zincs are indicated as large balls. The strands of the [1-sheet (l-V) and helices (A-C) are indicated. The heavy atoms of the inhibitor and residues of the protein that ligate zinc are shown. The inhibitor runs antiparallel to strand IV. The structural zinc lies above the (1-sheet and is... 

Figure 5.10 Ribbon diagram of the transferrin receptor dimer depicted in its likely orientation with regard to the plasma membrane. One monomer is blue, the other is coloured according to domain the protease-like, apical and helical domains are red, green and yellow respectively the stalk is shown in grey, connected to the putative membrane spanning helices in black. Pink spheres indicate the location of Sm3+ ions. Reprinted with permission from Lawrence et ah, 1999. Copyright (1999) American Association for the Advancement of Science.

The arrangement of the 24 subunits of the apoferritin molecule in their 432 symmetry viewed down a fourfold axis is presented in Figure 6.3. Also included in Figure 6.3 is a labelling scheme of symmetry related subunits and a representation of the subunit as a ribbon diagram of the -carbon backbone. Of the 174 amino-acid residues of the L-chain 140 (80 %) are found in five a-helices. Each of the 24 subunits consists... 

Fig. 5.1. Ribbon diagram of a fluorescent protein (citrine, PDB entry 1HUI) crystal structure. The chromophore is buried in the protein s interior and shown in balls and sticks representation.

Figure 1. Ribbon diagram of thermolysin complexed the inhibitor Cbz-GlyP-NH-Leu-Leu (stick) and Zn (sphere) in the active site (PDB code 5TMN).

Figure 2. A ribbon diagram of rhizopus pepsin (PDB code 5APR). The catalytically important Asp dyad (Asp218 and Asp35) side-chains are shown in stick diagrams. The P-hair pin flap that covers the active site cleft is located in the bottom of the diagram.

FIGURE 5-11 Ribbon diagram of an NBD dimer (PDB 160). 3 strands are depicted as arrows and a helices as coiled ribbons. The two nucleotides, shown as stick models, bind to form part of the interface that stabilizes the dimeric interaction. (With permission from Fig. 5 of reference [88].)... 

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