University of Southern Maine
Learn how to use Swiss-PdbViewer. Work through the
Topic: Electron Transport & Oxidative Phosphorylation
These views feature structures of some model compounds with redox
centers, and some molecules involved in oxidative
Electron Transport: Cast of Characters and Model Compounds
from the Protein Data Bank.
- Display a ribbon model of the backbone, along with wireframe
model of the heme prosthetic group. Color the ribbon by secondary
structure. What is the dominating structural element in this
- Display the heme and its neighbors to 5 angstroms.
- Find the histidine and methionine side chains that serve as
heme-iron ligands, and the two cysteine side chains that join the
heme covalently to the protein backbone.
- Color the charged side chains as follows: positive blue,
negative red. Notice that the side of the molecule with the
exposed heme edge shows a preponderance of positive charge. The
opposite side has more negative charges. As a result, cytochrome c
has a large dipole moment, which may function to orient the
molecule as it approaches its redox target.
- Is this a model of the reduced or oxidized form of cytochrome
c? Read the file header to find out.
- At the PDB, find the other member of this redox couple.
Download it and superimpose it on 5cyt. Are there substantial
conformational differences between the oxidized and reduced
Rieske Iron-Sulfur Protein
(solubile fragment from bovine heart mitochondria)
from the Protein Data Bank.
- Find and display the FeS center, along with its neighbors to 5
angstroms. What protein side chains provide ligands to the FeS
center? (SPV may not draw all the bonds in these complexes. You
can add them using Build: Add Bond.)
- Add a ribbon model of the remaining residues. What are the
main secondary structural elements?
Structures are also known for many small FeS proteins, most of
them ferredoxins. Here is a gallery of representative FeS centers
from ferredoxins. For each of these proteins, answer the same
questions as for the Rieske iron-sulfur protein. This will provide
you a tour of several common types of FeS centers.
Ferredoxin from Haloarcula marismortui
PDB file: 1DOI.pdb
Ferredoxin from Azotobacter vinelandii, oxidized form at
pH 6 ( Fe3S4 and
PDB file: 1FDA.pdb
Ferredoxin from Chromatium vinosum
PDB file: 1BLU.pdb
Cytochrome c Oxidase (Complex IV)
PDB File: 1OCC.pdb.
Download this file and explore it as you read about Complex IV in your text.
- Hide all residues and display a ribbon model. Color ribbon by
chain to distinguish chains. There are so many chains that SPV
runs out of colors for displaying them.
- Select and display HETATM groups only. Then zoom in on
individual sites, label them to learn their identity, and add
their neighboring ligands to the display. After adding neighbors,
display the van der Waals surface of the hetero group to help
distinguish it from its neighbors.
- To help you find hetero groups in the Control Panel, you can
use a little-known feature of SPV: hot typing. For
instance, if you display hetero groups and label them, you will
see that one of the hemes is designated HEA516. Activate the
Control Panel and quickly type 516. Then press return. Hem
516 is displayed, and it is also selected in the Control Panel.
The hot-typing feature is not documented.
Putative cytochrome c binding site and cytochrome c (for docking,
Configure your browser to use SPdbV for chemical/x-pdb file
before downloading these two files. Then download them in
succession, and SPdbV should display both.
- Binding Site: 1OCCBnd.pdb GLUs
and ASPs on proposed binding site colored red with VDW
- Cytochrome c: 3CYTChO.pdb
After downloading both files to SPdbV, on 3CYT, color LYS and ARG
blue with VDW surfaces. See if you "dock" the blue side chains of
cytochrome c onto the red side chains of cytochrome c oxidase. You
are exploring new territory: the exact mode of binding is not
F1-ATPase from bovine heart mitochondria
PDB File: 1COW.pdb.
Download this model and explore it as you read about this enzyme in your text.
The noncatalytic alpha subunits are chains A, B, and C. The
catalytic beta subunits are chains D, E, and F. The gamma subunit is
chain G. The ligands (space-filling) are ANP, a nonhydrolyzable ATP
analog (one in each of the three noncatalytic alpha subunits, and one
in the catalytic beta subunit F), ADP (in catalytic beta subunit D),
and the antibiotic ATPase inhibitor aurovertin B (in catalytic beta
subunits E and F). The catalytic sites are thought to be at the
interfaces between alpha and beta subunits, such as the site of ADP
binding in chain D.
- Set Prefs: Ribbons to show one only strand in ribbon
display. Then hide all residues and redisplay the model as ribbon.
Color ribbon by chain and identify the F1-ATPase subunits described
in your text.
- Display hetero groups (Select: Group Kind: HETATM
<return>). Identify the hetero groups and use them to
identify the catalytic sites in ATPase.
- Chain G is thought to rotate within the F1 alpha and beta
subunits and drive conformational changes that lead to ATP
synthesis. Attempts to observe such rotation recently met with
success (see this abstract
and Nature , Mar 20, 1997; vol 386, pp 217-219 and
299-302, ), demonstrating that the ATPase is indeed a molecular
rotary motor enzyme.
In mitochondria, the complete F1-FO complex
catalyzes the synthesis of ATP. For the study that produced this
model, the F1 cluster was severed from FO to
produce a crystallizable fragment. This fragment is called
F1-ATPase because it catalyzes hydrolysis of ATP,
presumably the reverse of the F1-FO-catalyzed
process. The structure shown is thought to be an ADP-inhibited form
of the ATPase, produced when ADP is present, but phosphate is absent.
Only parts of the gamma chain are visible in the electron-density map
obtained from x-ray crystallography. The other F1
components, the delta and epsilon subunits, are not visible, but they
have been revealed by more recent work (see this abstract).
The correspondence between the beta subunits observed and the three
postulated conformations in the catalytic cycle are open: F; loose:
E; tight: D. The ATP-synthase cycle for each subunit is open, loose,
tight, open ..., while the ATPase cycle is open, tight, loose, open,
.... In both directions, it is suggested that aurovertin B, an
uncompetitive inhibitor, acts to prevent attainment of the tight
The function of ATP binding to the noncatalytic alpha subunits is
Explore the structure further:
- Make a ribbon display of beta strands only. Color by chain.
Note the crown of beta barrels formed by the alpha and beta
- Explore contacts between the alpha/beta hexamer and the
central chain G. What types of residues predominate in these
contacts. What is the importance of this type of rotation for the
rotation of G within the alpha/beta hexamer?
- Examine the binding sites for nucleotides. Do they resemble
nucleotide binding sites in other nucleotide-binding proteins, for
For additional vivid illustrations of proton-pumping ATPases,
including some neat neat ATPase
animations, look at Siggi
Englebrecht's Home Page.
It Might Be Fun...
Use SwissPdbViewer to put the three alpha/beta pairs into separate
files (the three active sites are in these pairs: A/E, B/F, C/D).
Then superimpose them and study the differences between the open,
tight, and loose conformations. If you include the gamma subunit with
each file, you may be able to see how it exerts its influence on the
conformation of each active site.
(Information for this section taken from "The structure of bovine
F1-ATPase complexed with the antibiotic aurovertin B," van Raaij,
M.J., et al, Proc. Nat. Acad. Sci., 93,
6913-6917, 1996, and references 17 and 19 therein. The PDB code for
the complete structure file of the F1-ATPase is 1COW.)