The bc₁-complex

The catalytic subunits - overall view

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1. Show heme groups of cytochrome b as spacefilling models. Heme b_H is red; heme b_L is magenta.
2. Show histine ligands to the hemes as orange spacefilling models.
3. Show conserved glycines in helices A and C as white spacefilling models.
4. Show some of the residues which affect the Q_o-site when changed by mutagenesis,as ball and stick models in CPK-coloring. Stigmatellin, if present, is shown as an orange stick model
5. Show some of the residues which affect the Q_i-site when changed by mutagenesis, as ball and stick models in CPK-coloring. Q_i or antimycin, if present, are shown as yellow stick models.
6. Richardson cartoon of structure.
7. Spacefilling model of the catalytic subunits, with prosthetic groups. Cyt b, blue; cyt c₁, red; ISP, green; b-hemes, magenta; c-heme, dark red; Q_i or antimycin, yellow; stigmatellin, orange; others, cyan

Heme binding domains of cytochrome b

1. Zoom in on residues involved in ligation of hem b_L.
2. Zoom in on residues involved in ligation of hem b_H.

The inhibitor binding sites

The following models show the approximate positions of inhibitors or quinone, and features of the structure associated with the catalytic sites.

The following buttons will only work if the appropriate model is loaded.

1. Show the position of the Q_o-site occupant (if any) as a spacefilling model.
2. Show the position of Q_i or antimycin as a spacefilling model.
3. A more detailed look at the Q_i-site, with antimycin or quinone in place.
4. A more detailed look at the Q_o-site, with stigmatellin (or myxothiazol, or MOA-stilbene, or Q_o) in place.

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

Liganding of occupant at the Q_o-site

His-161 of 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:
1. The initial script may take up to several minutes (depending on processor and memory capacity) to generate the surface. Be patient!
2. Only the exterior surface is seen.

Generate surface. View of cyt b with Fe₂S₂, occupant, and heme b_L approximately in the screen plane.
Rotate 45^o around y-axis.  Rotate 45^o around x-axis.  Rotate 45^o around z-axis.
Rotate -45^o around y-axis.  Rotate -45^o 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)

Inhibitor resistance mutations.
1. Residues at the Q_i-site at which modification leads to inhibitor resistance.
   Yellow, Diuron and antimycin resistance;
   Orange, Diuron and HQNO resistance;
   Red, HQNO resistance;
   Brown, HQNO and funiculosin resistance;
   Green, funiculosin resistance or sensitivity;
   Cyan, antimycin and funiculosin resistance;
   Blue, antimycin resistance.
   Residues in CPK-coloring are heme ligands (H98, R101, and H197), or a possible ligand to Q_i (H202).
   
2. Residues at the Q_o-site at which modification leads to inhibitor resistance.
   Yellow, myxothiazol resistant sites;
   Red, stigmatellin resistance sites;
   Green, residues at which modification leads to resistance to both inhibitors.
   Stigmatellin is shown as a ball and stick model, colored light blue. The heme of cyt b_L is shown as a magenta wireframe model. The iron sulfur protein is shown in the stigmatellin induced configuration, as an orange backbone model.

See Table of data (Brasseur et al., 1996) from which the residues shown in these scripts have been selected.
3. Residues at which mutation produces a modified g_x band. 
   Yellow, normal occupancy but little or no rate; 
   Red, empty, but moderate rate; 
   Orange, different substitutions have either "red" or "yellow" effects; 
   Magenta, empty, and little or no rate; 
   Blue, some mutations are "magenta", and some "green-blue"; 
   Violet, partially occupied, slow rate, hyper sensitive to myxothiazol; 
   Green-blue, normal occupancy, moderate rate. 
   Also shown are residues (Leu-142 (brown) and Gly-143 (grey)) in the ISP at which mutation induced changes in the g_x=1.800 signal, and loss of rate. Heme is orange. Stigmatelin is shown as a ball and stick models in cyan.

See Table of data on which this script is based.
4. Residues in cytochrome b with which mutants at Gly-143 in ISP are expected to make contact. The Ca-atom of Gly-143 is colored white.
5. Residues in cytochrome b at the interface with the ISP are shown as stick models. Atoms close to the ISP are colored greenblue (within 5.0 Å), green (within 3.5 Å) or yellow (within 2.5 Å). Residues close to this interface at which mutation gives rise to a loss of the g_x=1.800 signal are shown as ball and stick models; atoms further away than 5.0 Å are blue. The DCCD-binding group Glu-163 is colored cyan. These residues are numbered at their Ca-atoms. Cytochrome b backbone is blue, ISP backbone is yellow.

For views of the residues on cytochrome b at the interface with ISP, and of the Q_o-site, with stigmatellin in place, either load one of the file with ISP in the stigmatellin position (above) or the complete complex
.

6. Turn labels off.

Physico-cemical views

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1. Spacefilling model colored to show residue polarity. Hydrophobic, white; polar, green; basic, blue; acidic, red.
2. ISP subunit colored to show degree of conservation of redisues. The color-coding is red -> yellow -> green -> greenblue -> blue, for most conserved to least conserved. Note that the cone of residues around the 2Fe2S center is completely conserved; this is the surface which docks in the cyt b interface.
3. Conservation profile of cyt b subunit. Note that the docking socket on cyt b for the SP is also highly conserved.

Show helices in cytochrome b

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1. Helix a, white Helix A, yellow Helix ab, green Helix B, blue-green
2. Helix bc, cyan Helix C, blue Helix cd, violet Helix D, orange
3. Helix E, orange-red -PEWYF-, white Helix ef, red
4. Helix F, gray Helix G, magenta Helix H, dark gray

H-bonding of some conserved residues

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Cytochrome b (Numbering is for avian mitchonrial complex)

Cytochrome c₁

1. Cartoon of cyt c₁ showing structure.
2. The heme binding residues.
3. Conserved acidic residues on cyt c binding face (?) and dimer interface.
4. Preliminary conservation profile of cyt c₁ subunit (the current assignment of side-chains is based on the bovine sequence, since the chicken sequence is not yet available).