Launch guide window

Launch NCBI Home Page

Goals

• Locate disordered residues in a PDB file
• Locate disordered residues in Cn3D
• Select and annotate metal-binding side chains

Steps

1. Retrieve the structure record
   
   • On the NCBI home page, click on the Structure link on the top tool bar.
   • Enter 1TFR in the search box and click Go.

2. View the Structure Summary page
   
   • Click on the accession number to open the structure summary page.
   • When was this structure submitted?
   • How many amino acids does this protein contain?

3. View the original PDB file
   
   • Click on the PDB code to view the PDB summary.
   • In the upper right portion of the page, click on the icon to the right of the PDB code (the icon looks like a paper document).

4. Locate disordered residues in the PDB file
   
   • Scroll down to REMARK 465 listing the missing residues.
   • Confirm the list by scrolling down to the ATOM records where the coordinates are listed. The residue number appears in the 5th column.

5. View the structure in Cn3D
   
   • Go back in your browser to the structure summary page for 1TFR.
   • Click the structure image.

6. Locate the N- and C-termini using Cn3D
   
   • In the structure window, choose Style / Edit Global style.
   • Uncheck the Strand and Helix Object boxes.
   • Click on the Labels tab, and check the termini box for Protein Backbone. Click Done.

7. Locate the disordered residues using Cn3D
   
   • Double click on the ends of the discontinuous parts of the structure (they should turn yellow).
   • Locate the highlighted residues in the Sequence/Alignment Viewer.
   • What color are the disordered (missing) residues in the sequence?

8. Select metal-binding residues
   
   • Position the mouse pointer over any residue in the sequence window, and find its number in the lower left panel of the window.
   • Select residues 19, 71, 132 and 155 by shift-clicking them in the sequence window.
   • Find the residues on the structure.
   • What heterogen is near these residues?

9. Create a custom annotation
   
   • In the structure window, choose Style / Annotate.
   • Click "New" and enter a name for the annotation.
   • Click "Edit Style" and uncheck the boxes next to Helix Objects and Strand Objects.

10. Display and label the side chains
    
    • Check the box next to Protein side chains, select "Tubes" from the menu to the right, and select a color of your choice.
    • Click on the Labels tab, and set the spacing to 1 under Protein Backbone.
    • Click Done, then OK, and Done.

11. Annotate a metal ion
    
    • Double click the nearby magnesium ion.
    • Create a second annotation using Style/Annotate, and color the magnesium ion as you like. Use the Heterogen row of controls.

12. View your annotations
    
    • In the structure window, choose Show/Hide / Show Selected Residues.
    • Double click in any white area of the sequence window to remove the highlighting.
    • Using the File menu, you can now save the file for future use.

Revised December 4, 2007