Complex III of Electron Transport Chain: Difference between revisions

Complex III of the electron transport chain has a dimeric structure with each monomer containing as many as 11 subunits, but the structure shown to the right has 9. <ref>1KYO.pdb - C.LANGE,C.HUNTE, PROC.NATL.ACAD.SCI.USA, '''99''', 2800, 2002 - is being used to generate the images in the first applet.  The 'default scene' green link available in the first 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. Follow the link to OCA in the green table below the applet for additional information on the complete complex and the peptide components.</ref> <scene name='Complex_III_of_Electron_Transport_Chain/View_one_subunit/3'>Coloring one monomeric unit grey</scene> reveals this dimeric structure.  Notice that one of the <font color='red'>peptides</font> of each subunit invades the space of the other monomeric unit. Labels show the orientation of the complex within the inner mitochondrial membrane. <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 green, blue and red are active in the electron transport chain. The grey peptides are not assigned a function in the mechanism of Complex III action, but they do have other catalytic activities and functions. 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), hinge domain - short segment between the membrane and head domains, and head domain - contains the Fe/S center and occupies space in the other monomeric unit. <br><br>

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>Since 1KYO.pdb contains stigmatellin bound at the Q_P sites, stigmatellin will be used to represent ubiquinol.  The 1KYO.pdb file was modified to generate this and the next several structures. 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 since it is empty in the PDB file, it 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='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.