Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Be sure to read the Introduction to the Biochemistry Graphics Gallery to learn how to view these files.
Topic: Electron Transport and Oxidative Phosphorylation
For graphics from other topics, see Topics List.
Set your browser to use RasMol for PDB files and RasMol scripts: See Configuring Netscape.
Molecules to Explore
These views feature structures of some molecules involved in oxidative phosphorylation, and some model compounds with redox centers.
Heme proteins Cytochrome c
The pdb file is 5cyt.pdb. Click on the file name to receive and display the file with RasMol. Then click on each script file name (.spt) when you are ready to view it.
View 1. 5cytTOON.spt A cartoon of cytochrome c, showing the histidine and methionine side chains that serve as heme-iron ligands, and the two Scysteine side chains that join the heme covalently to the proteinbackbone.
View 2. 5cytSChg1.spt The charged side chains, with charged atoms shown as spheres - 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.
View 3. 5cytSChg2.spt Spacefilling view, also emphasizing distribution of surface charges. Positive side chains are blue; negative side chains are red.
The next pdb file is 5cytHem.pdb, which includes only the coordinates of the heme and its neighbors. Click on the file name to download and display it in wireframe.
View 4. 5cytHem.spt View of the heme environment, emphasizing ligands and links to the backbone.
Iron-Sulfur Centers
No coordinates are currently available for FeS proteins from the mitochondrial electron e- transport chain. Structures are known, however, for several small FeSproteins, most of them ferredoxins. Here is a gallery of representative FeS centers from ferredoxins.
Ferridoxin from Haloarcula marismortui (Fe2S2)
Structure file: 1doi.pdb Click on the filename to view the entire structure in wireframe.
View 1. 1doiTOON.spt Cartoon emphasizing the iron-sulfur center.
Structure file for Views 2 and 3: 1doiFS2.pdb
View 2. 1doiFS2.spt Ball-and-stick view of Fe2S2center. Iron is red-orange, sulfide ion is yellow, cysteinesulfur is green.
View 3. 1doiFS2sf.spt Space-filling view of Fe2S2 center.
Ferredoxin from Azotobacter vinelandii, oxidized form at pH 6 ( Fe3S4)
Structure file: 1FDA.pdb Click on the filename to view the entire structure in wireframe.
View 1. 1fdaTOON.spt Cartoon emphasizing the two iron-sulfur centers, one Fe4S4 and one Fe3S4.
Structure file for Views 2 and 3: 1fdaFS3.pdb
View 2. 1fdaFS3.spt Ball-and-stick view of Fe3S4center. Iron is red-orange, sulfide ion is yellow, cysteine sulfur is green.
View 3. 1fdaFS3sf.spt Space-filling view of Fe3S4center.
Ferredoxin from Chromatium vinosum (Fe4S4)
Structure file: 1BLU.pdb Click on the filename to view the entire structure in wireframe.
View 1. 1bluTOON.spt Cartoon emphasizing the two Fe4S4 centers.
Structure file for Views 2 and 3: 1bluFS4.pdb
View 2. 1bluFS4.spt Ball-and-stick view of Fe4S4 center. Iron Fe is red-orange, sulfide S ion is yellow, cysteine sulfur is green. Notice a fifth cysteine near, but not covalently bonded to, the FeS center. You can see in the next view that this sulfur is in van der Waals contact with an iron Fe ion.
View 3. 1bluFS4sf.spt Space-filling view of Fe4S4center and the neighboring cysteine.
Cytochrome c Oxidase Under Construction: Pass At Your Own Risk
Configure your browser to use RasMol for chemical/x-pdb files. Run RasMol on your desktop or within the folder that receives downloaded files. Then download PDB files and Scripts in succession.
Alpha carbons and hetero groups:
· PDB File: 1OCCCAlpHets.pdb
· Script File: 1OCCAH.spt
Overview of Cytochrome c Oxidase Structure Add blather here
Hetero groups and neighbors
· PDB File: 1OCCRDX.pdb
· Script File: 1OCCRDXSites.spt
Description of Redox Sites Add blather here
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.pdbGLUs 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. End of Construction: Resume Normal Speed
F1-ATPase from bovine heart mitochondria
Structure file for View 1: 1cowBkBn.pdb Click on the filename to view the ligands of the protein. This file contains only the alpha carbons, and because RasMol always starts up with a wireframe view, the backbone is not on display. Select "Backbone" from the Display menu, or click the filename for View 1 to see the backbone.
View 1. 1cowBkBn.spt Backbone and ligands. The noncatalytic alpha subunits (chains A, B, and C) are dark blue, medium blue, and cyan. The catalytic beta subunits (chains D, E, and F) are green, yellow-green, and yellow. The gamma subunit (chain G) is orange. The ligands (space-filling) are ANP, a nonhydrolyzableATP analog (green in all three of the noncatalytic alpha subunits, and red in the catalytic beta subunit F), ADP (magenta in catalytic beta subunit D), and the antibiotic ATPaseinhibitoraurovertin B (cyan 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.
From this view, you can see that the three catalytic subunits have different ligand-binding affinities and (less obviously) different conformations. This observation supports the theory that each catalytic subunit cycles through three conformations (open, loose, tight, open, ...) in synthesizing ATP from ADP and phosphate. The conformational changes may be caused by rotation of the alpha/beta hexamer with respect to the central gamma subunit (G). The gamma subunit is the stalk that normally connects this F1cluster to the FO cluster, an integral protein in the inner mitochondrial membrane. Researchers believe that rotation of the alpha/beta cluster is driven by movement of protons H+ down the concentration and voltage E gradient maintained by electron e- transport. 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. 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.
Structure file for View 2: 1cowCrn.pdb Click on the filename to see the first domain of each alpha and beta subunit.
View 2. 1cowCrn.spt Cartoon of the crown at the top of the F1-ATPase. This crown is formed by six 6beta barrels, each the first domain of an alpha or beta subunit. Beta pleated-sheet overlap between the edges of successive barrels completes a circular, 24-strand, antiparallel pleated sheet structure. Subunit colors, aside from the color of the sheet strands, are the same as in View 1.
Structure file for View 3: 1cowGNbrs.pdb Click on the filename to see the gamma subunit and all atoms within 8 angstroms Å of it.
View 3. 1cowGNbrs.spt Space-filling model of gamma subunit and its contacts with the alpha/betahexamer. Mainchain colors of the subunits are the same as in View 1. Hydrophobic side chains in gamma are magenta, and hydrophobic side chains in the other subunits are purple. Slabbing is turned on, so hold down the "control" key and drag the mouse away from you to cut into the structure. Notice that most contacts are purple against magenta, which shows that the points of contact between G and the other subunits are hydrophobic. These contacts may "lubricate" the rotation of the hexamer around the gamma shaft.
Structure file for View 4: 1cowF.pdb Click on the filename to see the catalytic beta subunit (chain F) in wireframe.
View 4. 1cowF.spt Cartoon of chain F (open?), with bound ANP (ATP analog) and aurovertin. The alpha and beta subunits contain three domains, with main chains colored green, orange, and white. Helices are cyan and sheets are magenta in all domains. Domain 1 is a barrel of twisted antiparallel beta strands (part of the crown described above). Domain 2 is a nucleotide-binding domain, with a parallel beta sheetsandwiched between alpha helices. Domain 3, where the antibiotic binds, is mostly alpha-helical.
Structure file for View 5: 1cowFNuBnd.pdb Click on the filename to see the ANP binding site of subunit F in wireframe.
View 5. 1cowFNuBnd.sptANP and its binding region in subunit F. The dark green atom is Mg2+ bound to the ATP analog. A short section of backbone colored cyan marks the end of an alpha helix whose dipole interacts with the ATP phosphates. This alpha helix is common to nucleotide-binding domains. Most of the contacts with the adenine ring are hydrophobic. Several polar and charged groups surround the polar triphosphate group. It is not known which, if any, of these groups are involved in catalysis.
It Might Be Fun...
Obtain the full structure file (1COW -- a biggie, so get it with a fast connection), and 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 looseconformations. 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 antibioticaurovertin 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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