Complex III of Electron Transport Chain: Difference between revisions

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<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.


<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>1BGY.pdb was modified to contain only the six active subunits (chains c, d, e, o, p, q) and their cofactors.  1BGY.pdb contains no cofactors bound at Q<sub>P</sub> or Q<sub>N</sub> so these binding sites are shown as one large open surface which outlines all four binding sites as pockets.</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 <scene name='Complex_III_of_Electron_Transport_Chain/Posit_c1_1bgy/1'>Cyto c1 position</scene>, 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. 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/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>1BGY.pdb was modified to contain only the six active subunits (chains c, d, e, o, p, q) and their cofactors.  1BGY.pdb contains no cofactors bound at Q<sub>P</sub> or Q<sub>N</sub> so these binding sites are shown as one large open surface which outlines all four binding sites as pockets.</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 <scene name='Complex_III_of_Electron_Transport_Chain/Posit_c1_1bgy/1'>Cyto c1 position</scene>, 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. 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.


== Q Cycle ==
== Q Cycle ==
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==View Interior of Q Binding Sites==  
==View Interior of Q Binding Sites==  
<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'  />The applet on the right shows the interior cavities of Complex III with the four Q sites labeled.  (<scene name='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'>Reset initial scene.</scene>) The PDB file used to generate the display has no cofactors binding at these sites so they are empty.  After turning on the Slicer observe that as the surface is rotated its interior is exposed and that there are interior chambers connecting the different binding sites.
<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'  />The applet on the right shows the interior cavities of Complex III with the four Q sites labeled.<ref name=1BGYmodified/> (<scene name='Complex_III_of_Electron_Transport_Chain/1bgy_qsite_surfaces/3'>Reset initial scene.</scene>)
<jmol>
<jmolButton>
~slab=false
<script>if (~slab);slab off;~slab=false;else;slab on;~slab=true;endif;</script>
<text>Toggle Slicer</text>
</jmolButton>
</jmol>
 
The PDB file used to generate the display has no cofactors binding at these sites so they are empty.  After turning on the Slicer observe that as the surface is rotated its interior is exposed and that there are interior chambers connecting the different binding sites.


==Notes and References==
==Notes and References==
<references/>
<references/>
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