Retinol-Binding Protein: Beta-Barrel Structure
The retinol-binding protein is a beta-barrel structure that is used to hold and
transport the lipid alcohol vitamin A (retinol) through the blood stream
The three-dimensional structure of this single chain protein has been
solved by x-ray crystallography
and can be loaded into the ProteinShader program by selecting Open from the
and then using the file chooser box to select the 1AQB.pdb file.
When the retinol-binding protein is first loaded, it will be displayed as a
pen-and-ink style drawing of ribbons and tubes. To switch to an all tubes
style display as shown in Figure 1A, go to the
above the canvas and select Tubes from the Cartoon submenu. Regions of regular
secondary structure such as beta-strands and alpha-helices are shown with a
greater radius (1.5 angstroms) than general loop regions (0.75 angstroms).
To switch from the Figure 1A image to the Figure 1B image, first go to the
above the canvas and use the Cartoon submenu to go back to Ribbons and Tubes.
Next, go to the
of the Control Panel on the right side of the canvas and click on the
β-Strands radio button to select all beta-strands. Then select Hatching
1 from the Bend Texture menu, which will change the texture map that is
applied to the middle of each segment of the ribbon that corresponds to an
To fade out the loop regions that connect the beta-strands, go to the menu at
the top right of the Control Panel and use it to change from 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.
To switch from the Figure 1B image to the Figure 1C image, go to the
above the canvas and select Top. The image will be close to that seen
in Figure 1C, but you will have to left click and drag the mouse across the
canvas a little to move the protein into the same view as in Figure 1C.
The original view can always be restored by going to the
above the canvas and selecting Original. To zoom in on an image, use
the scroll wheel or center mouse button. If the canvas has the focus (because
it was clicked on), pressing the "i" key once will zoom the camera in
by 5 angstroms, while the "o" key will zoom the camera out by 5
Figure 1. Pen and ink style illustrations of the retinol-binding protein.
(A) Side view of this beta-barrel structure shown as tubes with halftoning.
(B) Same as in part A, but with the beta-strands and loops shown as ribbons,
and with the loop regions set to 75% translucency. (C) Same as in part B, but
with the image rotated to show an open end of the beta-barrel. The larger of
the two tube-shaped helical structures seen in this view is a gamma-helix,
while the smaller is an alpha-helix (gamma-helices are represented the same
way as alpha-helices in a cartoon-style display).
The images were captured as described in the
section of the tutorials main page.
Space filling style displays
To display a space filling style view of the retinol-binding protein,
it might be a good idea to first select Open from the
and reload the 1AQB.pdb file (only to be sure that you are starting with all of
the default settings for the structure). After the protein reloads it will be
displayed again as tubes and ribbons. Now go to the
above the canvas and use the Atom submenu to select Space Filling. By default,
the ProteinShader program only shows amino acids when a structure is first
loaded, so go to the
above the canvas to select Heterogens Allowed and Waters Allowed. After using
above the canvas to set the background to black, the image should look the same
as in Figure 2A. To see the retinol molecule (a heterogen) buried in the
center of the beta-barrel (Figure 2B), go back to the
above the canvas to deselect Amino Acids Allowed and Waters Allowed.
To simplify the space filling style display of the retinol-binding protein,
first go back to the
and reselect Amino Acids. Then use the menu at the top right of the Control
Panel to select the
Atom Visibility subpanel,
and select Model-AA from the Selected menu at the top of the subpanel. Click
on the Invisible button in the bottom half of the panel to make all of the amino
acid atoms invisible. To show just the beta-strands, first click on the
β-Strands radio button. Then go to the Apply To menu in the middle of the
subpanel and select Backbone. Clicking on the Opaque button should now cause
the backbone atoms (N, CA, and C) of the beta-strands to become visible.
To change the color of the beta-strand atoms, go back to the menu at the top
right of the Control Panel and switch from the
Atom Visibility subpanel
Atom Color subpanel.
With the β-Strands radio button still selected, click on the Chooser button
to open a color chooser dialog box and select a shade of green. The image
should now match Figure 2C. To get a better look at the retinol molecule
inside of the barrel, drag the mouse across the canvas to rotate the image
until something similar to Figure 2D is obtained. The retinol can also be
shown in a cartoon-style display of tubes and ribbons, where it will be
shown in space filling form (it did not show up in Figure 1 only because the
Heterogens Allowed item in the
above the canvas had not been selected yet).
Brandon C, Tooze J: Beta Structures.
In Introduction to Protein Structure. 2nd edition.
New York: Garland Publishing; 1998: 67-88.
Zanotti G, Berni R:
Plasma retinol-binding protein: structure and interactions with
retinol, retinoids, and transthyretin.
Vitam Horm 2004, 69: 271-295.
Zanotti G, Panzalorto M, Marcato A, Malpeli G, Folli C, Berni R:
Structure of pig plasma retinol-binding protein at 1.65 A resolution.
Acta Crystallogr, Sect D, 1998, 54: 1049-1052.
Retinol-binding protein PDB entry 1AQB