Complex III of Electron Transport Chain: Difference between revisions

UNDER CONSTRUCTION <br>

'''Be aware''' that the structure in the first applet is large and significant time is required for loading the structure! The other applets load much faster.

Complex III of the electron transport chain contains as many as 11 subunits per monomer.  The structure shown to the right has 9. <ref>1KYO.PDB is being used to generate the images in the first applet.  The 'default scene' green link available in the Jmol applet shows the dimer structure along with Heavy Chain (Vh) Of Fv-Fragment, Light Chain (Vl) Of Fv-Fragment and Cytochrome C, Iso-1 all of which are a part of 1KYO.PDB. The link to OCA in the green box below contains additional information on the complete complex and the individual peptide components.</ref> <scene name='Complex_III_of_Electron_Transport_Chain/Labels_applied/3'>Show orientation</scene> of the complex within the inner mitochondrial membrane with labels. <scene name='Complex_III_of_Electron_Transport_Chain/View_one_subunit/3'>Coloring one monomeric unit grey</scene> reveals that one of the <font color='red'>peptides</font> of each subunit invades the space of the other subunit. <scene name='Complex_III_of_Electron_Transport_Chain/View_3_active_subunits/4'>Three of the subunits</scene> of each monomeric unit have a direct role in the passage of electrons in the respiratory chain. The subunits that are colored are active in the electron transport chain. The grey peptides have other catalytic activities and functions, and the interior spaces which are created by the positions of the other subunits have a role in the movement of the substrates from one active site to another active site within the complex. The two subunits of cytochrome b (colored green) for the most part are buried in the complex and have minimal exposure to the intermembrane space and matrix.  <font color='#0000CD'>Cytochrome c1 subunits</font> are positioned on top of cytochrome b and their outer surfaces are exposed to the intermembrane space.  They are held in place by helical tails that extend deep into the complex and membrane. The <font color=red>Rieske subunits</font> are Fe/S proteins with three domains: membrane domain (long helical segment that extends into the membrane), head domain which contains the Fe/S center and hinge domain (short segment between the other two).

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_L for low potential, and the other two are called b_H for high potential. Each of the cytochrome b's have two binding sites for substrate. [http://en.wikipedia.org/wiki/Ubiquinol Ubiquinol] and the inhibitor stigmatellin bind at one of these sites, Q_P, (<font color='red'>Stigmatellin</font> is shown in the applet below.<ref>The structure shown in the second applet was produced by modifying 1KYO.pdb. The Jmol command 'write file' was used to make a PDB file that contained only the 6 active subunits and cytochrome c (chains c,d,e,n,o,p,w) and the cofactors of those peptides.</ref>), and the site is adjacent to the b_L heme (<scene name='Complex_III_of_Electron_Transport_Chain/Stigmatellin/1' target='second'>return to view of the stigmatellin</scene>). The other site, Q_N, binds [[Coenzyme_Q10|ubiquinone]], and this site is outlined by <scene name='Complex_III_of_Electron_Transport_Chain/Surface_antimycin/1' target='second'>a surface with pockets</scene> which is located adjacent to the b_H heme.  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 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_P 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_P 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 here 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, COMPLETE STRUCTURE OF THE 11-SUBUNIT OVINE MITOCHONDRIAL CYTOCHROME BC1 COMPLEX, ''SCIENCE'', '''281''', 64, 1998. 1BGY.PDB was modified to contain only the six active subunits (chains c, d, e, o, p, q)and their cofactors.</ref>  that does not have stigmatellin bound at Q_P, so the surface of the binding sites is shown in orange and the black arrow is pointing to the Q_P pocket.  This pocket is on a straight line between the hemes of cyto c1, as in the view showing the cyto b position, but the Fe/S center is removed from the Q_P 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.

<applet load='1bgy_modified.pdb' size='400' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1' /> At the start of the cycle the Q_P site is empty and the Fe/S center of the Rieske protein is in the Int position. (<scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_arrowless/1'>Reload initial scene</scene>) With the binding of <scene name='Complex_III_of_Electron_Transport_Chain/Posit_intermed_1bgy_cycle/2'>ubiquinol</scene>, UQH₂, to cytochrome b (black arrow) the Rieske protein flexes at the hinge region rotating the Fe/S head so that the His which is bound to the Fe/S also <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle/1'>binds to the ubiquinol</scene> at Q_P (<font color=red>stigmatellin</font> in this model).  Binding of the His to UQH₂ reduces its pK, and the [http://en.wikipedia.org/wiki/Ubiquinol UQH₂] loses a proton to become UQH^{<big> -</big>}.  The position of Q_P in the complex is such that the proton which is lost <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_arrow/1'>diffuses to the intermembrane space</scene>. After UQH₂ loses the proton and becomes UQH^-, it passes an electron through the His to the Fe⁺³ reducing it to Fe⁺².  With the loss of the electron the UQH^{<big> -</big>} becomes UQH<big>^•</big>, a [http://en.wikipedia.org/wiki/Ubiquinone#Chemical_properties semiquinone], which loses a proton and becomes UQ^{<big> • -</big>}, the conjugate base of the semiquinone.  The proton diffuses to the intermembrane space, as the first one did.  (The fate of the semiquinone can be traced starting with the next paragraph.) After Fe in the Fe/S center is reduced by the UQH^{<big> -</big>}, the Rieske head rotates & the Fe/S moves to cytochrome c1, <scene name='Complex_III_of_Electron_Transport_Chain/Posit_cyto_b_cycle_move_c1/1'>the "c1" position</scene>, so that the second His bound to Fe/S binds to the heme of cytochrome c1. When the His contacts the heme of cytochrome c1 an electron is rapidly passed from the Fe/S through the His to the Fe of the cytochrome c1 heme, and since it is now in the oxidized form, the Rieske protein returns to the "Int" position. The cytochrome c1 heme is now reduced, and when <scene name='Complex_III_of_Electron_Transport_Chain/Cyto_c_2_cycle/1'>cytochrome c binds</scene> to it the electron is passed from the c1 heme to the c heme (black arrow). The cytochrome c then releases from the membrane and diffuses through the intermembrane space to Complex IV.  

The UQ^{<big> • -</big>}, the <scene name='Complex_III_of_Electron_Transport_Chain/Focus_semiuq/1'>conjugate base</scene> of the semiquinone, which was formed at Qp as described above and is shown here as <font color=red>stigmatellin</font> is oxidized to the full UQ when it <scene name='Complex_III_of_Electron_Transport_Chain/Electron_semi_to_hem_l/2'>passes an electron</scene> to heme b_L. The <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_l_to_hem_h/1'>electron</scene> is then passed from the Fe of heme b_L to the Fe of Heme b_H, and with Heme b_H being next to UQ bound at the Q_n site (Binding site is shown as a <scene name='Complex_III_of_Electron_Transport_Chain/Hem_h_next_to_surface/3'> surface</scene>.), the <scene name='Complex_III_of_Electron_Transport_Chain/Electron_hem_h_to_uq/3'>electron</scene> is passed to UQ. With only one electron being passed in this series of reaction the UQ is reduced to UQ^{<big> • -</big>}, and becomes UQH<big>^•</big> when it accepts a <scene name='Complex_III_of_Electron_Transport_Chain/Proton_matrix_in/1'>proton</scene> which comes from the matrix. The end products of the first half of the Q cycle are an ubiquinol oxidized to ubiquinone at the Q_p site, a reduced cyt c and an ubiquinone reduced to semi-ubiquinone at the Q_n site.  

The second half of the Q cycle is different form the first half in that at the Q_n site at the end of the cycle a semi-ubiquinone is reduced to ubiquinol so that during a complete cycle at the Q_n site an ubiquinone is reduced to ubiquinol.

SUMMARY:<br>

2 ubiquinols oxidized at the Q_p<br>

1 ubiquinone reduced to ubiquinol<br>

==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/1'  />

==Footnotes==