Complex III of Electron Transport Chain: Difference between revisions

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== Structure of three active components ==
== Structure of three active components ==
Each cytochrome b contains<scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_b/5'> two hemes</scene> (displayed as spacefill and colored cpk). Identify each of the hemes by toggling 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<sub>L</sub> for low potential, and the other two are called b<sub>H</sub> for high potential. Each of the cytochrome b's have two substrate binding sites. [http://en.wikipedia.org/wiki/Ubiquinol Ubiquinol] and the inhibitor stigmatellin bind at Q<sub>P</sub>, one of these two sites, (<font color='red'>Stigmatellin</font> is shown at this site in the applet below.<ref name=1KYOmodified>Since 1KYO.pdb contains stigmatellin bound at the Q<sub>P</sub> sites, stigmatellin will be used to represent ubiquinol.  This structure and the next several are generated by a modification of 1KYO.pdb. The Jmol command 'write file' was used to make a PDB file that contains only the 6 active subunits and cytochrome c (chains c,d,e,n,o,p,w) and the cofactors of those peptides.</ref>), and the site is adjacent to the b<sub>L</sub> heme (<scene name='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' target='second'>Reset initial scene </scene>). The other site, Q<sub>N</sub>, is located adjacent to the b<sub>H</sub> heme and binds [[Coenzyme_Q10|ubiquinone]], and since it is empty in the PDB file, it is shown as <scene name='Complex_III_of_Electron_Transport_Chain/Surface_antimycin/1' target='second'>a surface with pockets</scene>.  In this view you are looking into the lit pocket in which the ubiquinone binds. You can rotate the structure and observe the ubiquinone binding pocket in the other subunit.
Each cytochrome b contains<scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_b/5'> two hemes</scene> (displayed as spacefill and colored cpk). Identify each of the hemes by toggling 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<sub>L</sub> for low potential, and the other two are called b<sub>H</sub> for high potential. Each of the cytochrome b's have two substrate binding sites. [http://en.wikipedia.org/wiki/Ubiquinol Ubiquinol] and the inhibitor stigmatellin bind at Q<sub>P</sub>, one of these two sites, (<font color='red'>Stigmatellin</font> is shown at this site in the applet below.<ref name=1KYOmodified>Since 1KYO.pdb contains stigmatellin bound at the Q<sub>P</sub> sites, stigmatellin will be used to represent ubiquinol.  This structure and the next several are generated by a modification of 1KYO.pdb. The Jmol command 'write file' was used to make a PDB file that contains only the 6 active subunits and cytochrome c (chains c,d,e,n,o,p,w) and the cofactors of those peptides.</ref>), and the site is adjacent to the b<sub>L</sub> heme (<scene name='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' target='second'>Reset initial scene </scene>). The other site, Q<sub>N</sub>, is located adjacent to the b<sub>H</sub> heme and binds [[Coenzyme_Q10|ubiquinone]], and since it is empty in the PDB file, it is shown as <scene name='Complex_III_of_Electron_Transport_Chain/Surface_antimycin/1' target='second'>a surface with pockets</scene>.  In this view you are looking into the lit pocket in which the ubiquinone binds. You can rotate the structure and observe the ubiquinone binding pocket in the other subunit.


<applet load='1kyo_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' name='second' caption='1KYO modified/>Each <font color='#0000CD'>cytochrome c1</font> contains <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/5'>a heme</scene>. Viewing <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_rotate/1' target='second'>cyto c1 in spacefill</scene> 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 on the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_side_open/3'>side next to the Rieske protein</scene> (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 <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_rotate/1'>surface of cyto c1</scene>. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/3'>negatively charged acidic residues</scene> which attrack the complementary positive charges on cytochrome c, a basic protein. <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_1/1'>Cytochrome c</scene> <font color='cyan'>(colored cyan)</font> bound to one cyto c1 as viewed from intermembrane space and from slice through membrane <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2/2'>showing that the hemes</scene> of the two cytochromes are in close contact.  The <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_transparent/1'>two hemes</scene> seen through transparent spacefill.
<applet load='1kyo_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' name='second' caption='1KYO modified/>Each <font color='#0000CD'>cytochrome c1</font> contains <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/5'>a heme</scene>. Viewing <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_rotate/1' target='second'>cyto c1 in spacefill</scene> 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 on the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_side_open/3'>side next to the Rieske protein</scene> (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 <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_rotate/1'>surface of cyto c1</scene>. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/3'>negatively charged acidic residues</scene> which attrack the complementary positive charges on cytochrome c, a basic protein. <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_1/1'>Cytochrome c</scene> <font color='cyan'>(colored cyan)</font> bound to one cyto c1 as viewed from intermembrane space and from slice through membrane <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2/2'>showing that the hemes</scene> of the two cytochromes are in close contact.  The <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_transparent/1'>two hemes</scene> seen through transparent spacefill.
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