User:Angel Herraez/Sandbox 1

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'''Be aware''' that the data files used in this tutorial are large and significant time is required for loading structures!
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== Test for the sequence widget ==
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== Structure of three active components ==
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<seqtool/>
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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 toogling 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 binding sites for substrate. Ubiquinol binds at one of the sites, Q<sub>P</sub>, and the inhibitor <font color='red'>stigmatellin</font> also binds at this site in both cytochrome b's (<font color='red'>stigmatellin</font> seen in the applet below) (<scene name='Complex_III_of_Electron_Transport_Chain/Sma_cyto_b1/2' target='second'>return to view of the stigmatellin</scene>), and the site is adjacent to the b<sub>L</sub> heme. The other site, Q<sub>N</sub>, binds [[Coenzyme_Q10|ubiquinone]], and <scene name='Complex_III_of_Electron_Transport_Chain/Surface_qn/3' target='second'>this surface</scene> outlines the site which is adjacent to the b<sub>H</sub> heme. antimycin A.
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<StructureSection size='350' side='right' caption='initial scene from Karsten' scene='37/376372/Overall/3'>
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Initial scene is a copy of User:Karsten_Theis/Showcase
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<scene name='33/337412/Cartoon_and_ligands/1'>1ea5, one chain with 2 ligands </scene>
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<applet load='1kyo' size='400' color='black' frame='true' align='right' scene ='Complex_III_of_Electron_Transport_Chain/Sma_cyto_b1/2' name='second'/>Each <font color='#0000CD'>cytochrome c1</font> contains <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1/3'>a heme</scene>. Viewing <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_top/2' 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 to the <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_side_open/1'>side facing 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_top/2'>surface of cyto c1</scene>. There are <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c1_neg_res/1'>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/Hem_cyto_c/3'>Cytochrome c</scene> <font color='cyan'>(colored cyan)</font> bound to one cyto c1 showing that the hemes of the two cytochromes are in close contact. The <scene name='Complex_III_of_Electron_Transport_Chain/Hem_cyto_c_transparent/1'>two hemes</scene> seen through transparent spacefill.
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<scene name='33/337412/Dimer_cartoon/1'>hemoglobin dimer</scene>
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<scene name='Complex_III_of_Electron_Transport_Chain/Fes/2'>Fe/S center</scene> is in the head of the Rieske protein. Each of the Fe/S centers is complexed with <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his/1'>two His</scene>. As a result of bending at the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_hinge/2'>hinge region</scene> the head can be in one of three possible positions. Here the Fe/S head is in the so called <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytob/3'>cyto b position</scene>, because a His of the Fe/S/His complex is in contact with the ubiquinol bound at the Q<sub>P</sub> site of cyto b. Of course in this model, <font color='red'>stigmatellin</font> is binding at Q<sub>P</sub>, and the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_his_sma525/1'>His is in contact with stigmatellin</scene>. The <scene name='Complex_III_of_Electron_Transport_Chain/Load_1bgy/2'>Int position</scene> is intermediate between the other two positions. This view is generating by 1BGY.pdb, and it does not have stigmatellin bound at Q<sub>P</sub>, so the Rieske protein is in the Int conformation rather than the cyto b conformation. Notice that in the Int position the Fe/S/His complex is not in contact with the <font color='red'>Q<sub>P</sub> site</font>, but it is closer to the heme of cyto c1. In the cyto c1 position the <scene name='Complex_III_of_Electron_Transport_Chain/Fes_posit_cytoc1/2'>other His</scene> of the Fe/S/His is hydrogen bonded to a carboxylate oxygen of the heme in c1.
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<scene name='33/337412/Hemoglobin_tetramer/1'>hemoglobin tetramer</scene> has chains A, B, "A-2" and "B-2"
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</StructureSection>

Current revision

Test for the sequence widget

initial scene from Karsten

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

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