Complex III of Electron Transport Chain: Difference between revisions

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Karl Oberholser, Eran Hodis, Jaime Prilusky, Alexander Berchansky, Michal Harel

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 <applet load='1kyo_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/5' name='second' caption='1KYO modified/>Each <font color='#0000CD'>cytochrome c1</font> contains a heme (<scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/5' target='second'>Reset initial scene </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 is the gray heme embedded in each of the cyto c1's showing that the heme is located in a crevice which has an opening to the intermembrane space and an opening 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). The opening seen in this view permits the cyto c1 heme to make contact with the Rieske protein, and the one on the  <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_rotate/1'>surface of cyto c1</scene> permits contact with cytochrome c when it binds to  cytochrome c1 at the intermembrane surface. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/3'>negatively charged acidic residues</scene> which attract the complementary positive charges on cytochrome c, a basic protein. Cytochrome c <font color='cyan'>(colored cyan)</font> bound to one cyto c1 as viewed from <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_1/1'>intermembrane space</scene> and from <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2/2'>slice through membrane </scene> showing that the hemes 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.
-<scene name='Complex_III_of_Electron_Transport_Chain/Fes/4'>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_2_his/1'>two His</scene>. As a result of bending at the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_hinge/4'>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/Posit_cytob_closeup/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/Posit_cyto_b/2'>cyto b position</scene>'. Notice that the His of the <font color='red'>Rieske head</font> is in contact with <font color='red'>stigmatellin</font> in the Q<sub>P</sub> site and the stigmatellin is positioned on a straight line between the two hemes in the cyto c1 subunits. The '<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy/3'>Int position</scene>' is shown with a PDB file <ref>S.Iwata, J.W.Lee,K.Okada,J.K.Lee, M.Iwata, B.Rasmussen, T.A.Link, S.Ramaswamy, B.K.Jap, ''Science'', '''281''', 64, 1998</ref><ref name=1BGYmodified>The pdb file used for this scene and those of the next couple were generated by a modification of 1BGY.pdb. It contains data for only the six active subunits (chains c, d, e, o, p, q) and their cofactors.  The pdb file contains no substrates or inhibitors bound at Q<sub>P</sub> or Q<sub>N</sub> so the computed surface of these interior spaces is one large surface which outlines all four binding sites.</ref>  that does not have stigmatellin bound at Q<sub>P</sub>, and the black arrow is pointing to the Q<sub>P</sub> pocket.  This pocket is on a straight line between the hemes of cyto c1, as the Q<sub>P</sub> site was positioned in the previous view of the 'cyto b position', but the Fe/S center is not in contact with the Q<sub>P</sub> binding pocket and is in a position intermediate between the cyto b and cyto c1 positions. In the 'Cyto c1 position', the third position, the second His of the Fe/S is in contact with the cyto c1 heme through a hydrogen bond to a carboxylate oxygen of the heme, but since it can not be shown directly, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_c1_1bgy/1'>here</scene> a black arrow indicates the direction of  movement from 'Int position' to the 'Cyto c1' position, and an 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/4'>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_2_his/1'>two His</scene>. As a result of bending at the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_hinge/4'>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/Posit_cytob_closeup/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/Posit_cyto_b/2'>cyto b position</scene>'. Notice that the His of the <font color='red'>Rieske head</font> is in contact with <font color='red'>stigmatellin</font> in the Q<sub>P</sub> site and the stigmatellin is positioned on a straight line between the two hemes in the cyto c1 subunits. The '<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy/4'>Int position</scene>' is shown with a PDB file <ref>S.Iwata, J.W.Lee,K.Okada,J.K.Lee, M.Iwata, B.Rasmussen, T.A.Link, S.Ramaswamy, B.K.Jap, ''Science'', '''281''', 64, 1998</ref><ref name=1BGYmodified>The pdb file used for this scene and those of the next couple were generated by a modification of 1BGY.pdb. It contains data for only the six active subunits (chains c, d, e, o, p, q) and their cofactors.  The pdb file contains no substrates or inhibitors bound at Q<sub>P</sub> or Q<sub>N</sub> so the computed surface of these interior spaces is one large surface which outlines all four binding sites.</ref>  that does not have stigmatellin bound at Q<sub>P</sub>, and the black arrow is pointing to the Q<sub>P</sub> pocket.  This pocket is on a straight line between the hemes of cyto c1, as the Q<sub>P</sub> site was positioned in the previous view of the 'cyto b position', but the Fe/S center is not in contact with the Q<sub>P</sub> binding pocket and is in a position intermediate between the cyto b and cyto c1 positions. In the 'Cyto c1 position', the third position, the second His of the Fe/S is in contact with the cyto c1 heme through a hydrogen bond to a carboxylate oxygen of the heme, but since it can not be shown directly, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_c1_1bgy/2'>here</scene> a black arrow indicates the direction of  movement from 'Int position' to the 'Cyto c1' position, and an orange arrow indicates the direction of movement from the 'Int position' to the 'Cyto b position'.
 == Q Cycle ==