Interactive Tutorial (requires CHIME plug-in)

This interactive tutorial requires that readers have the Chime plug-in (version 2.0. or higher) installed, and that their browser has been configured appropriately to recognize the Chime MIME type. Full instructions are available at the following URLs:

To rotate about x or y axis, use left mouse-button, move pointer on image.
To rotate about z axis, use Shift and right mouse-button, move pointer horizontally.
To zoom, use Shift and left mouse-button; move down to zoom in, up to zoom out.
To pan , use Ctrl and right mouse-button.
To slice when in Slab Mode, use Ctrl and left mouse-button.
For other menu items , click on picture with right mouse-button. 
  • Rotation Start and Stop
  • Display options, including various rendering options
  • Other options, including Slab Mode, Specular rendering, Select

    • Coloring options
Click the buttons below to load the structures indicated. Each structure is a "functional" 3-subunit monomer. 
Native complex with UQ (Q i) and three detergents (1bcc, revised). 
Structure with antimycin and stigmatellin (3bcc, revised). 
Structure with stigmatellin and UQ (Q i) (2bcc). 
Structure with myxothiazol and UQ (Q i) (unpublished). 
Model with quinol at the Q o-site to replace the inhibitor in the stigmatellin structure (from 2bcc). 
Model with quinone at the Q o-site to replace the inhibitor in themyxothiazol structure.  		Stereo
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Rotation
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Pathways for proton release from the Qo -site of the bc1 -complex- scroll down for tutorial

Note. For technical reasons arising from the formating of interactive web pages, this tutorial cannot be presented in frame format. See links below for hints on 3-D viewing, and information about the Chime plug-in.

The structures from coordinates of the bc 1-complex from chicken heart mitochondria (Zhang et al. 1998, and Berry E.A. and colleagues, unpublished).

In the initial view, the three catalytic subunits of the native complex are shown, colored by chain. The subunits shown are those that interact during catalysis, -a functional monomer. The protein is shown as a backbone model, and prosthetic groups are wireframe models, colored as follows:hemes bH (top) and bL , magenta; heme c1 ,red; Fe2 S2 cluster, space filling CPK-colored spheres;Qi , yellow; phospholipids and detegent, cyan.

The N-phase (mitochondrial matrix or bacterial cytoplasm) is at the top, and the P-phase (intermembrane space or periplasm) at the bottom.

The catalytic subunits - overall view

    Restore wireframe view
     
  1. Show heme groups of cytochrome b as space filling models. Heme bH is red; heme bL is magenta.
  2. Show histine ligands to the hemes as orange space filling models.
  3. Richardson cartoon of structure.
  4. Space filling model of the catalytic subunits, with prosthetic groups. Cyt b, blue; cytc 1, red; ISP, green; b-hemes, magenta; c-heme, dark red; Q ior antimycin, yellow; Q o-site occupant, orange; others, cyan

Heme binding domains of cytochrome b

  1. Zoomin on residues involved in ligation of hem bL .
  2. Zoomin on residues involved in ligation of hem b H.

The inhibitor binding sites

Thespans contributing to the Qo -site. Helix C (C-terminal end),blue; cd-helix, blue-green; ef-loop, green; -PEWY- , yellow; ef-helix,orange; helix F (N-terminal end), red. Stigmatellin (or other occupant if present, white), and heme bL (magenta) as space filling models. Spans shown are those predicted from modeling studies, and sites of inhibitor resistance.
Thespans contributing to the Qi -site. Helix a and aA-loop, blue;helix A (N-terminal end), green blue; helix B (heme ligation), cyan; helix D (C-terminal end), green; de-loop, yellow; helix E (N-terminal end), orange.Antimycin or Qi (white) and cyt bH (magenta) as space filling models. Spans shown are those predicted from modeling studies, and sites of inhibitor resistance.

Liganding of occupant at the Qo -site

His-161of ISP and Glu-272 of cyt b, - ligands involved in proton processing, simple view.

Show surface of protein with Q o-site occupant in place,and His-161 of ISP and Glu-272 of cyt b as ligands .

    (Note: the initial script may take up to several minutes (depending on processor and memory capacity) to generate the surface. Be patient!Only the exterior surface is seen.)
Generate surface. View of cyt b with Fe 2S 2, occupant, and heme b L approximately in the screen plane.
Rotate45 o around y-axis.  Rotate 45o around x-axis. Rotate 45 o around z-axis.
Rotate-45 o around y-axis.  Rotate -45o around x-axis. Rotate -45 o around z-axis.
    Hint: Rotation, pan, zoom, and slab, work much faster with the surface turned off.
Surface off Surface on  Surface transparent (toggle)

White background, black labels. Black background, white labels.

 

Hints on 3-D viewing