Ed Berry's structure of the bc1-complex
(Chicken heart mitochondria)

Spectra and Crystals of the bc1-complex from Ed Berry, and the Q-cycle mechanism. 


   This site contains information, links, pictures, and down-loadable materials based on research on the bc1 complex. This group of electron transfer enzymes, - generally known as bc1 complexes in mitochondria, bacterial respiratory chains and photosynthetic bacteria, or b6f complexes in the photosynthetic chains of oxygenic photosynthesis, - carries the main flux of energy through the biosphere.

  The annual synthesis (and consumption) of biomass in the biosphere represents a storage of energy 20-100 fold greater than all human energy usage, including fossil fuels and nuclear power. Because of inefficiencies in energy conversion, the flux in the biosphere is about 1000-fold greater than that through all anthropogenic processes.

   In the interests of rapid dissemination of research materials within the group, some of the material accessible through this site is made available before publication. It is expected that any use of such material will be appropriately acknowledged. 

A brief description of what the complex does, and how.

Follow the links below to find additional information.

Recent publications

Coordinate data files

The bc1 complex in Chime, using special versions of the coordinates.

The Berry/Kim group (structures abstracted from files 1BCC, 2BCC, 3BCC, together with structures containing myxothiazol or MOA-stilbene) and the Iwata/Jap group (structures P65 and P6522, available as files 1BE3 and 1BGY) have made coordinates of their structures available through the bc1 complex homepage. For the Berry/Kim group, the deposited files, together with equivalent files of the full dimeric complex, and files of "functional" 3-subunit monomers are available. For the Iwata/Jap group, the coordinates of the dimeric complex of both their structures are available. Both sets of structures can be downloaded through the link from this page, or by anonymous ftp. These files do not contain the preamble of the PDB files, and do not have Hetero atoms separately defined, or connection matrices.

In the Chime tutorials (below), features of interest are accessible through buttons. Tutorials are available for the 3-subunit "functional" monomer, and also for the dimeric complexes. The former can be used to explore features of mechanistic interest.

The third link below is to a "working model" showing a speculative mechanism from the Crofts group, demonstrated through a Chime animation. The model is heavily annotated, with justification for the different assumptions underlying the mechanism, together with references to the literature. The model is based on the Zhang et al. structures, but incorporates different configurations of the ISP from both the Zhang et al. and Iwata et al. coordinates, and additional models (quinone species at the Qo-site, electrons and protons) necessary for the animation.

The Zhang et al. bc1 complex structures

The Iwata et al. bc1 complex structures .

A speculative model of the Q-cycle mechanism for the bc1 complex

Mechanism in Chime (~0.9 MB)

Mechanism in an annotated animated GIF (~4 MB, but runs as it loads)

Mechanism in an annoted AVI movie (~6.7 MB)

Get Chime here.

The Zhang et al. coordinates for the chicken heart mitochondrial bc1 complex

A brief summary of the files (1bcc.pdb, 1bccdimref.pdb, 1bcc_m.pdb, 3bcc.pdb, 3bccdimref.pdb, 3bcc_m.pdb) is available here (see also 1bcc3bcc.txt).

The Iwata et al. coordinates for the beef heart mitochondrial bc1 complex

The files are p65.pdb and p6522.pdb

Lab Home Pages

UHDBT analogs from Bernie Trumpower

Structure of cytochrome f from Bill Cramer and Janet Smith, in a brief Chime tour.

The PROMISE (Prosthetic groups and Metal Ions in Protein Active Sites) Database

with a new page on the bc1 complex.

Mauro Degli Esposti's Cytochrome b alignments



Cytochrome b mutants

A Compilation of Mutations located in the Cytochrome b Subunit of the Bacterial and Mitochondrial bc1 Complex, by Gael Brasseur, A. Sami Saribas and Fevzi Daldal (1996) Biochim. Biophys. Acta 1275, 61-69.
Text of the paper
Table 1a
Table 1b


Gordon Research Conferences


John Allen
Britton Chance
Crofts Lab
Diego Gonzalez-Halphen
Fevzi Daldal
Les Dutton
Guenter Hauska
Jonathan Marder
Werner Mäntele
Sabine Metzger-Groom
Bob Niederman
Peter Nicholls
Tomoko Ohnishi
Graham Palmer
Matti Saraste
Vlad Shinkarev
Bernie Trumpower
Chang-An Yu

Les Dutton's cartoons of the UPenn Biochemistry and Biophysics faculty. 

E-mail addresses

The bc1 complex e-mail address list


This directory can be accessed by anonymous ftp.

The FTP site is available for downloading of any information deposited there. However, the directory accessed here is read-only for anonymous access. To upload files using anonymous ftp, click to the uploads directory. However, this site is write-only for anonymous access. Members of the bc1-complex group have read-write access to both directories.

For details on group policy, e-mail site coodinator (see below).

The bc1-Complex site has been chosen as HMS Beagle's "Web Pick of the Day" (Oct-28-98).

Other useful sites

Biophysics Links

e-mail to Site Coordinator