Ribonuclease Inhibitor: Alpha/Beta Horseshoe-Shaped Structure [PDB:2BNH]

The ribonuclease inhibitor protein is a horseshoe-shaped structure that is built from a repeating leucine-rich motif that corresponds to a beta-strand/loop/alpha-helix unit [1, 2, 3, 4]. These units are arranged so that the inside part of the horseshoe contains a parallel beta-sheet, while alpha-helices form the outside part. The three-dimensional structure of the porcine ribonuclease inhibitor has been solved by x-ray crystallography [2, 3], and can be loaded by selecting Open from the File menu of the ProteinShader program and then using the file chooser box to select the 2BNH.pdb file.

Cartoon-style displays with halftoning

When the ribonuclease inhibitor is first loaded, it will be displayed as a pen-and-ink style drawing of ribbons and tubes as shown in Figure 1A. In the default orientation, the beta-strands (wide ribbons) are mostly obscured by the alpha-helices (spiral tubes), but the mouse can be dragged across the canvas to rotate the image and get a better sense of the protein's three-dimensional structure. The protein can be returned to its original orientation at any time by going to the Orientation menu menu above the canvas and selecting Original.

To switch from the Figure 1A image to the Figure 1B image, first drag the mouse horizontally or vertically across the canvas to get a side view of the horseshoe shape. Then go to the Decorations subpanel of the Control Panel on the right side of the canvas, and click on the β-Strands radio button to select All beta-strands. Next, use the Halftone Texture menu right below the Halftoning button to select a Vertical Bars pattern to map onto the surface of the beta-strand ribbons, and set the Bend Texture menu to None (the bend texture is applied to the middle of each segment of the ribbon that corresponds to an amino acid, and the intensity of the bend texture is scaled according to how curved the ribbon or tube segment is).

To fade out the loop regions that connect the beta-stands, go to the menu at the top right of the Control Panel and use it to change from the Decorations subpanel to the Cartoon Visibility subpanel. Click on the Loops radio button to select all loops, and then click on the Translucent button. By default, the button should be set to use 75% translucency, but the value can be changed by using the slider control below the button.

A [2BNH.pdb tubes] B [2BNH.pdb tubes and ribbons]

Figure 1. The ribonuclease inhibitor protein is a horseshoe-shaped structure. (A) A ribbons and tubes display of this single-chain protein using halftoning to produce a pen-and-ink style drawing. (B) The protein has been rotated to a view that makes the horseshoe shape more obvious. Beta-strands are shown as ribbons with stripes, and they form the inner part of the horseshoe shaped structure, while alpha-helices are shown as tubes, and they form the outer part of the horseshoe. The loop regions are shown as semi-transparent thin ribbons. The images were captured as described in the Saving Images section of the tutorials main page.

Cartoon-style displays with color

The Decorations subpanel can also be used to select color images for ribbons and tubes, as seen in Figure 2. To set the beta-strands to a color image with a pattern mapped onto the surface of the ribbons, first select the β-Strands radio button, and then click on the Patterns button. The menu right below the Patterns button is set to Vertical Bars by default, but can be changed to any of several other images. The default region color for beta-strands is green, but they can be set to any color (or colored by amino acid type) by using the Cartoon Color subpanel.

To change the alpha-helices to match Figure 2, select the Helices button near the top of the Decorations subpanel, and then click the Plain button at the very bottom of the panel (plain here means color images with no special patterns mapped onto the surfaces of the ribbons and tubes). The default region color for alpha-helices is red, but as with beta-strands and loops, the Cartoon Color subpanel can be used to set them to any color, and the background color of the canvas can be changed to black by using the Background menu above the canvas.

A [2BNH.pdb color] B [2BNH.pdb wireframe]

Figure 2. Color images of the ribonuclease inhibitor protein. (A) The protein is presented in the same view as Figure 1B, but with beta-strands shown as green ribbons with black stripes and alpha-helices as red tubes. Specular highlighting (the shiny plastic-like appearance) is used to enhance the three-dimensionality of the images. (B) The image in part A has been rotated so that the open end of the horseshoe is closest to the viewer. For tubes and ribbons shown in color, a blue end cap marks the amino-terminus, while a red end cap marks the carboxyl terminus. The images were captured as described in the Saving Images section of the tutorials main page.


1. Brandon C, Tooze J: Alpha/Beta Structures. In Introduction to Protein Structure. 2nd edition. New York: Garland Publishing; 1998: 47-65.

2. Kobe B, Deisenhofer J: Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol 1996, 264: 1028-1043.

3. Ribonuclease inhibitor protein PDB entry 2BNH [http://www.rcsb.org/pdb/explore/explore.do?structureId=2BNH]

4. Kobe B, Kajava AV: The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 2001, 11: 725-732.