User:Amy Kerzmann/Sandbox 8

From Proteopedia

What do you do when the pdb code only provides the monomeric form of a protein, but you can see a dimeric, trimeric or other higher-order structure on the PBD site?

Well, first you need to determine if that multimeric structure is just an artistic rendering of the molecule or if there is a file containing the 3-D structure.

For example, if you are interested in the Potassium Channel KcsA-Fab complex, you might include a structure window box on your Proteopedia page that displays 1k4c. This file will display the protein in a monomeric state, as shown here.

However, if you go tothe PDB and search for 1k4c, you'll be greeted with a tetrameric view of the same protein.

If you can click on "View in Jmol" and see a 3-D structure that you can manipulate, you are in luck! You will have the ability to represent the "biological assembly" or multimeric state of the protein on your Proteopedia page.

While on the "view in Jmol" page where you can see your 3-D structure, look toward the upper-right hand corner just above the structure window. You should see a drop-down menu titled "Download Files". Click on that menu and select "Biological Assembly gz (A)". This naming system reveals that the multimeric structure is an author-generated representation, not the actual crystallographic asymmetric unit of the protein.

Once that file has downloaded, you'll have to upload it to Proteopedia. MAKE SURE YOU DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION!

Back in Proteopedia, edit your page and open the "Scene authoring tools". Select the tab to "load molecule". Below the "From Proteopedia uploaded file:" box, there is a link to upload a file; click on it. Complete the upload screen, being very careful to remember EXACTLY what you name the file. The file name should end in ".pdb" or something similar. Return to the "load molecule" tab and type the name of the file into the "From Proteopedia uploaded file:" box. When you click "load", the multimeric structure should appear in the preview window toward your right.

Yay!

Oh, wait. Yours didn't load as multimer? Are you sure?

Take a look at the preview structure window. What is the name of your currently loaded file? It should be 1K4C_tetramer.pdb, no matter what you named the file when you uploaded it. If it is, that's a good sign. Now click on the Jmol icon in the corner of the structure window. The second line should read "model 1/4". Move your cursor over those words to reveal a submenu. Tick the "All" box. The preview image should immediately change to the tetrameric view.

Yay! :)

Now you can manipulate that image and use it to display the protein and your on your Proteopedia page.

It would be good to reference the author's construction of the biological assembly on PDB... Which I still need to do!