Complex III of Electron Transport Chain: Difference between revisions
| Line 8: | Line 8: | ||
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. One of these two sites, Q<sub>P</sub>, binds [http://en.wikipedia.org/wiki/Ubiquinol ubiquinol] or the inhibitor stigmatellin (<font color='red'>Stigmatellin</font> is shown at this site in the applet below.<ref name=1KYOmodified>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. Since 1KYO.pdb contains stigmatellin bound at the Q<sub>P</sub> sites, stigmatellin will be used to represent ubiquinol at Q<sub>P</sub> in the modified pdb file. </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. One of these two sites, Q<sub>P</sub>, binds [http://en.wikipedia.org/wiki/Ubiquinol ubiquinol] or the inhibitor stigmatellin (<font color='red'>Stigmatellin</font> is shown at this site in the applet below.<ref name=1KYOmodified>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. Since 1KYO.pdb contains stigmatellin bound at the Q<sub>P</sub> sites, stigmatellin will be used to represent ubiquinol at Q<sub>P</sub> in the modified pdb file. </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 | <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 has openings to the intermembrane space, as seen here, 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). 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'>Risieke 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/2'>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'>Risieke 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/2'>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'. | ||