User:Angel Herraez/Sandbox 1

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Structure of three active components

Each cytochrome b contains (displayed as spacefill and colored cpk). Identify each of the hemes by toogling off the spin and hovering the curser over an atom of the heme. Hem 501 and Hem 502 are in one cytochrome b, and Hem 521 and Hem 522 are in the other one. The two hemes in each cytochrome b are in different environments and therefore have different properties, e.g. reduction potential. Hemes 501 & 521 have a lower potential than the other two and are called b_L for low potential, and the other two are called b_H for high potential. Each of the cytochrome b's have two binding sites for substrate. Ubiquinol binds at one of the sites, Q_P, and the inhibitor stigmatellin also binds at this site in both cytochrome b's (stigmatellin seen in the applet below) (), and the site is adjacent to the b_L heme. The other site, Q_N, binds ubiquinone, and outlines the site which is adjacent to the b_H heme. antimycin A.

spinqualitylabelsall models PDB ID 1kyo Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Each cytochrome c1 contains . Viewing as it would be seen from the intermembrane space, there is an opening in the center of the dimeric c1 through which one can see the gray hemes of the cyto b's. Also seen in this view is the gray heme embedded in each of the cyto c1's showing that the heme is located in a crevice which is open to the intermembrane space and to the (heme oxygens are seen). These openings of the crevice permits the cyto c1 heme to make contact with the Rieske protein and with cytochrome c when it binds to the . There are which attrack the complementary positive charges on cytochrome c, a basic protein. (colored cyan) bound to one cyto c1 showing that the hemes of the two cytochromes are in close contact. The seen through transparent spacefill.

is in the head of the Rieske protein. Each of the Fe/S centers is complexed with . As a result of bending at the the head can be in one of three possible positions. Here the Fe/S head is in the so called , because a His of the Fe/S/His complex is in contact with the ubiquinol bound at the Q_P site of cyto b. Of course in this model, stigmatellin is binding at Q_P, and the . The is intermediate between the other two positions. This view is generating by 1BGY.pdb, and it does not have stigmatellin bound at Q_P, so the Rieske protein is in the Int conformation rather than the cyto b conformation. Notice that in the Int position the Fe/S/His complex is not in contact with the Q_P site, but it is closer to the heme of cyto c1. In the cyto c1 position the of the Fe/S/His is hydrogen bonded to a carboxylate oxygen of the heme in c1.