Crystal structure rhodopsin

Fig. 5. Models of the receptor-G protein complex. Two representations of receptor-G protein complexes are shown. The R Ga(0) fly complex created by manually docking the G protein onto an activated receptor model based on the rhodopsin crystal structure (1GZM) (left panel). Sites on Got that cross-link to residue S240 (cyan sphere) on the receptor are highlighted (cyan). This sort of data will be critical for improving models of the receptor-G protein complex, as it provides constraints for the location of IC 3 relatively to Ga. In this model, the nucleotide-binding pocket is some 30 A away from the receptor-binding surface. The model of an Ro Ga (O) [jy-com pIex is based on coordinates generously provided by K. Palczewski (published in Fotiadis et al, 2004).

Fig. 2. A 5-HT2A-receptor model constructed from the rhodopsin crystal structure. Serotonin is shown as a space-filled structure. Magenta colored backbone traces represent modeled structures of low reliability (N-terminus, C-terminus, and i3) as well as segments generated by insertion into or deletion of rhodopsin residues (el, e2, e3, and i3 loops). Stick structures of the side chains of conserved residues (yellow), ligandbinding site residues (red), and residues involved in receptor activation are shown. (Illustration appears in color in insert that follows p. 240.)...

A 5-HT2A-receptor model constructed from the rhodopsin crystal structure. Chapter 8, Fig. 1, p. 260 ... 

Fig. 9. Proximity relationships for residues in Cl relative to 316 in H8. Example of R1 distance mapping in rhodopsin. For each distance measurement, only two R1 side chains were in the protein, one fixed at the reference site 316, and the other at a site in the sequence 55-75. The R1 side chains were modeled based on crystal structure data with energy minimization subject to the experimentally determined distance constraint (shown). In each case, the measured distances in solution were in good agreement with those expected from the rhodopsin crystal structure. Substituted cysteine residues 65 and 68 most rapidly formed disulfide cross-links with the reference cysteine at 316 in H8. This is indicated by the dark bars connecting the potential disulfide partners.

Numerous insightful reviews detail the use of the rhodopsin crystal structure as a model building template for other class A GPCRs (Archer et al., 2003 Ballesteros et al., 2001 Becker et al., 2003 FUipek et al, 2003). Modeling studies of GPCR structure have been advanced to such an extent that ab initio structure prediction methods using the minimum possible experimental structural information are underway (Vaidehi et al., 2002). 

Figure 7.15. Rhodopsin crystal Structure. Three-dimensional structure of ihodopsin based on X-ray crystallography (186). Note that all-trans-retinal is protected fbm the intradiscal side by multiple structural elements, including several strands. Carbohydrates are in blue, 11 -cis-retinal is in green, and helices are in gray. Red shadows are added for esthetic reasons. This figure was generated by C. Behnke (UniversityofWashington)and is reprinted with permission from Prog. Retin, B/q Res., 20, 469-521 (2001).See color insert.

Fig. 8 Two-dimensional DARR NMR spectra of retinal-EL2 interactions. Rows from the two-dimensional DARR NMR spectra of rhodopsin black) and Meta II red) are shown. The rhodopsin crystal structure gray) with the Meta II model orange) obtained from molecular dynamic simulations are shown in the middle of the figure. Adapted from [18] with permission from Nature Publishing Group...

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