Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. Work through the Swiss-PdbViewer Tutorial.

Topic: Electron Transport & Oxidative Phosphorylation


These views feature structures of some model compounds with redox centers, and some molecules involved in oxidative phosphorylation.

Electron Transport: Cast of Characters and Model Compounds

Cytochrome c

Download 5cyt.pdb 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 protein?
  • 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 forms?

Iron-Sulfur Centers

Rieske Iron-Sulfur Protein

(solubile fragment from bovine heart mitochondria)

Download 1RIE.pdb 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 (Fe2S2)

PDB file: 1DOI.pdb

Ferredoxin from Azotobacter vinelandii, oxidized form at pH 6 ( Fe3S4 and Fe4S4)

PDB file: 1FDA.pdb

Ferredoxin from Chromatium vinosum (Fe4S4)

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, SwissPdbViewer)

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 surfaces.
  • 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 known.


Oxidative Phosphorylation

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 conformation.

The function of ATP binding to the noncatalytic alpha subunits is not known.

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 subunits.
  • 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 instance, dehydrogenases?

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.) 

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