Potassium Channel: Transmembrane Alpha-Helices [PDB:1BL8]

The potassium channel is an integral membrane protein composed of four subunits that form a single central pore that is selectively permeable to K+ ions [1, 2]. Each subunit is a single polypeptide chain that includes three alpha-helices: two transmembrane helices and one that faces the pore. The Streptomyces lividans potassium channel, which has sequence similarity to all known K+ channels, has been solved using x-ray crystallography [3, 4], and can be loaded loaded into the ProteinShader program by selecting Open from the File menu and then using the file chooser box to select the 1BL8.pdb file.

Cartoon-style displays with halftoning

When the potassium channel protein is first loaded, it will be displayed as a pen-and-ink style drawing of ribbons and tubes. To obtain something closer to the images in Figure 1, first go to the Style menu above the canvas and select Ribbons from the Cartoon submenu. Then go to the Decorations subpanel, and with Model showing in the menu under the Selected radio button, select Vertical Bars from the Halftone Texture menu and None from the Bend Texture menu. To fade out the loop regions, switch from the Decorations subpanel to the Cartoon Visibility subpanel and click on the Loops radio button before pressing the Translucent button. The degree of translucency can be adjusted with the slider control below the button.

The structure of the potassium channel is roughly cone-shaped, and has been compared to the petals of a flower that opens towards the outside of the cell [1], as shown in Figure 1A. To obtain this same view, first go to the Orientation menu above the canvas and select Back, and then left-click with the mouse and drag horizonally across the canvas to the left for a short distance. The center mouse button (or scroll wheel) can be used to zoom in a little, and the right mouse button can be used to translate the entire image up or down or side to side (see the Mouse Motion Control section for details and for Macintosh single-button mouse options).

The crystal structure of the potassium channel has three K+ ions and one water in the channel. To see these atoms, first go to the Visibility menu above the canvas and select Heterogens Allowed and then Waters Allowed. In the orientation shown in Figure 1B, only one of the K+ ions can be seen, so use the Orientation menu above the canvas to select Left, and then drag the mouse vertically downwards on the canvas a short distance to get something similar to Figure 1C, where all three K+ ions plus the oxygen of a water molecule are visible.

A [1BL8.pdb ribbons outside cell view] B [1BL8.pdb ribbons plus K+] C [1BL8.pdb side view]

Figure 1. Ribbons style display of the potassium channel, a transmembrane protein with an overall shape roughly like a cone. (A) The larger diameter end of the cone as seen from outside of the cell. Alpha-helices are shown as wide ribbons, while loop regions are translucent. (B) Same as part A, but with a K+ ion visible in the channel. (C) Same as part B, but with a side view where the end of the channel that faces outside the cell is on the right. Three K+ ions (deep pink) and a single water (red) inside the channel are now visible (hydrogen atoms are not shown). The images were captured as described in the Saving Images section of the tutorials main page.


1. Brandon C, Tooze J: Membrane Proteins. In Introduction to Protein Structure. 2nd edition. New York: Garland Publishing; 1998: 223-250.

2. MacKinnon R: Potassium channels. FEBS Lett 2003, 555: 62-65.

3. Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R: The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 1998, 280: 69-77.

4. Potassium channel PDB entry 1BL8 [http://www.rcsb.org/pdb/explore/explore.do?structureId=1BL8]