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.
description of what the complex does, and how.
Follow the links below to find additional information.
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.
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)
The Zhang et al. coordinates for the chicken heart mitochondrial bc1
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
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.
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
Gordon Research Conferences
Les Dutton's cartoons
the UPenn Biochemistry and Biophysics faculty.
The bc1 complex e-mail address list
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