Complex III of Electron Transport Chain: Difference between revisions

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<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 to the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_side_open/2'>side facing 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/Hem_cyto_c/4'>Cytochrome c</scene> <font color='cyan'>(colored cyan)</font> bound to one cyto c1 showing that the hemes 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' 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 to the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_side_open/2'>side facing 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/Hem_cyto_c/4'>Cytochrome c</scene> <font color='cyan'>(colored cyan)</font> bound to one cyto c1 showing that the hemes 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> the head can be in one of three possible positions.  Here the Fe/S head is in the so called <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytob/5'>cyto b position</scene>, because a His of the Fe/S/His complex is in contact with the ubiquinol bound at the Q<sub>P</sub> site of cyto b. Of course in this model, <font color='red'>stigmatellin</font> is binding at Q<sub>P</sub>, and the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his_sma525/2'>His is in contact with stigmatellin</scene>. The <scene name='Complex_III_of_Electron_Transport_Chain/Load_1bgy/3'>Int position</scene> is intermediate between the other two positions. This view is generating by 1BGY.pdb, and it does not have stigmatellin bound at Q<sub>P</sub>, 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 <font color='red'>Q<sub>P</sub> site</font>, but it is closer to the heme of cyto c1. In the cyto c1 position the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytoc1/2'>other His</scene> of the Fe/S/His is hydrogen bonded to a carboxylate oxygen of the heme in c1.
<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> 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 this view in order to compare it to the next scene. The <scene name='Complex_III_of_Electron_Transport_Chain/Load_1bgy/3'>Int position</scene> is intermediate between the other two positions. This view is generating by 1BGY.pdb, and it does not have stigmatellin bound at Q<sub>P</sub>, so the Rieske protein is in an intermediate conformation rather than the cyto b conformation.  Notice that in the Int position the Fe/S/His complex is not in contact with the <font color='red'>Q<sub>P</sub> site</font>, but it is closer to the heme of cyto c1. In the cyto c1 position the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytoc1/2'>other His</scene> of the Fe/S/His is hydrogen bonded to a carboxylate oxygen of the heme in c1.


== Q Cycle ==
== Q Cycle ==
<applet load='1kyo' size='400' color='black' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Sma_525_red/1' name='third'/>The cycle starts with the binding of UQH<sub>2</sub>, ubiquinol, to cytochrome b at a Q<sub>P</sub> site. In the applet to the right the Q<sub>P</sub> site is binding <font color=red>stigmatellin</font>. This binding causes the Rieske protein to flex at the hinge region rotating the Fe/S head so that the His which is bound to the Fe/S also binds to the UQH<sub>2</sub> at Q<sub>P</sub>.  Binding of the His to UQH<sub>2</sub> reduces its pK, and the quinol loses a proton.  The position of Q<sub>P</sub> in the complex is such that the proton which is lost diffuses to the intermembrane space.
<applet load='1kyo' size='400' color='black' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Sma_525_red/1' name='third'/>The cycle starts with the binding of UQH<sub>2</sub>, ubiquinol, to cytochrome b at a Q<sub>P</sub> site. In the applet to the right the Q<sub>P</sub> site is binding <font color=red>stigmatellin</font>. This binding causes the Rieske protein to flex at the hinge region rotating the Fe/S head so that the His which is bound to the Fe/S also binds to the UQH<sub>2</sub> at Q<sub>P</sub>.  Binding of the His to UQH<sub>2</sub> reduces its pK, and the quinol loses a proton.  The position of Q<sub>P</sub> in the complex is such that the proton which is lost diffuses to the intermembrane space.
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