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 binding sites for substrate. [http://en.wikipedia.org/wiki/Ubiquinol Ubiquinol] binds at one of the sites, Q<sub>P</sub>, and the inhibitor <font color='red'>stigmatellin</font> also binds at this site in both cytochrome b's (<font color='red'>stigmatellin</font> seen in the applet below)(<scene name='Complex_III_of_Electron_Transport_Chain/Sma_cyto_b1/2' target='second'>return to view of the stigmatellin</scene>), and the site is adjacent to the b<sub>L</sub> heme. The other site, Q<sub>N</sub>, binds [[Coenzyme_Q10|ubiquinone]], and <scene name='Complex_III_of_Electron_Transport_Chain/Surface_cn/1' target='second'>this surface</scene> outlines this site which is adjacent to the b<sub>H</sub> heme.  In this view you are looking into the lit pocket in which the ubiquinone binds. You can rotate the structure and observe the 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 binding sites for substrate. [http://en.wikipedia.org/wiki/Ubiquinol Ubiquinol] binds at one of the sites, Q<sub>P</sub>, and the inhibitor <font color='red'>stigmatellin</font> also binds at this site in both cytochrome b's (<font color='red'>stigmatellin</font> seen in the applet below)(<scene name='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' target='second'>return to view of the stigmatellin</scene>), and the site is adjacent to the b<sub>L</sub> heme. The other site, Q<sub>N</sub>, binds [[Coenzyme_Q10|ubiquinone]], and <scene name='Complex_III_of_Electron_Transport_Chain/Surface_antimycin/1' target='second'>this surface</scene> outlines this site which is adjacent to the b<sub>H</sub> heme.  In this view you are looking into the lit pocket in which the ubiquinone binds. You can rotate the structure and observe the binding pocket in the other subunit.




<applet load='1kyo' size='400' color='black' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Sma_cyto_b1/2' name='second'/>Each <font color='#0000CD'>cytochrome c1</font> contains <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/4'>a heme</scene>. Viewing <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_top/3' 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/2'>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_top/3'>surface of cyto c1</scene>. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/2'>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_2/1'>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/Hem_cyto_c/4'>showing that the hemes</scene> of the two cytochromes are in close contact.  The <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c_transparent/2'>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'/>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_top/3' 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/2'>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_top/3'>surface of cyto c1</scene>. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/2'>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_2/1'>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/Hem_cyto_c/4'>showing that the hemes</scene> of the two cytochromes are in close contact.  The <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c_transparent/2'>two hemes</scene> seen through transparent spacefill.


<scene name='Complex_III_of_Electron_Transport_Chain/Fes/3'>Fe/S center</scene> is in the head  of each <font color='red'>Rieske protein</font>. Each of the Fe/S centers is complexed with <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his/2'>two His</scene>. As a result of bending at the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_hinge/3'>hinge region</scene> (colored cyan) the head can be in one of three possible positions.  Here the Fe/S head is in the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his_sma525/2'>cyto b position</scene> in which a His of the Fe/S/His complex is in contact with the ubiquinol (actually <font color='red'>stigmatellin</font> in this model) bound at the Q<sub>P</sub> site of cyto b. Wider view of <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytob/6'>cyto b position</scene>. Make a mental snap shot of how close the <font color='red'>Risieke head</font> and Fe/S center is to cyto b (green) and Q<sub>P</sub> site (red spacefill) in order to compare it to the next scene. The <scene name='Complex_III_of_Electron_Transport_Chain/Load_1bgy/4'>Int position</scene> is intermediate between the other two positions. This view is generated by 1BGY.pdb and takes longer to load since a new pdb file is loading, and it does not have stigmatellin bound at Q<sub>P</sub> (colored teal), therefore the Rieske protein is not as close to cyto b but is in an intermediate position between cyto's b & c1. The <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_c1_arrow/3'>third position</scene> is the Cyto c1 position in which the Fe/S contacts the cyto c1 heme through the second His which is hydrogen bonded to a carboxylate oxygen of the heme in c1. Black arrow indicates the direction of  movement from Int position to the Cyto c1 position, and the orange arrow indicates the direction of movement from the Int position to the Cyto b position.
<scene name='Complex_III_of_Electron_Transport_Chain/Fes/3'>Fe/S center</scene> is in the head  of each <font color='red'>Rieske protein</font>. Each of the Fe/S centers is complexed with <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his/2'>two His</scene>. As a result of bending at the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_hinge/3'>hinge region</scene> (colored cyan) the head can be in one of three possible positions.  Here the Fe/S head is in the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his_sma525/2'>cyto b position</scene> in which a His of the Fe/S/His complex is in contact with the ubiquinol (actually <font color='red'>stigmatellin</font> in this model) bound at the Q<sub>P</sub> site of cyto b. Wider view of <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytob/6'>cyto b position</scene>. Make a mental snap shot of how close the <font color='red'>Risieke head</font> and Fe/S center is to cyto b (green) and Q<sub>P</sub> site (red spacefill) in order to compare it to the next scene. The <scene name='Complex_III_of_Electron_Transport_Chain/Load_1bgy/4'>Int position</scene> is intermediate between the other two positions. This view is generated by 1BGY.pdb and takes longer to load since a new pdb file is loading, and it does not have stigmatellin bound at Q<sub>P</sub> (colored teal), therefore the Rieske protein is not as close to cyto b but is in an intermediate position between cyto's b & c1. The <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_c1_arrow/3'>third position</scene> is the Cyto c1 position in which the Fe/S contacts the cyto c1 heme through the second His which is hydrogen bonded to a carboxylate oxygen of the heme in c1. Black arrow indicates the direction of  movement from Int position to the Cyto c1 position, and the orange arrow indicates the direction of movement from the Int position to the Cyto b position.
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