Browsing the Protein Data Bank and Viewing 3-D structures

The goal of this tutorial is to learn how to download PDB files

and manipulate them with the graphics program RASMOL.

RASMOL= Graphics Program to display and to show atomic molecular structures in three dimensions.

PDB = Protein Data Bank = Web Based Depository of 3Dimensional atomic data solved by NMR and X-ray crystallography.

CHIME = Shows molecular structures like RASMOL but inside a web page. It can be used to animate molecules on the web and as an educational resource. Chime uses the same rasmol commands.

We will use the OXYTRICHA 1.5 Quadruplex structure for this demo.

The structure is a dimer of GGGGTTTTGGGG the 12 Gs form the core of the quadruplex and the T regions form loops on the top and the bottom.

You can think of the quadruplex as letter U interlocking on another letter U.

The Residues are numbered G1 G2 G3 G4 T5 T6 T7 T8 G9 G10 G11 G12 for the first strand and G13 G14 G15 G16 T17 T18 T19 T20 G21 G22 G23 G24

for the second strand.

A) DOWNLOADING PDB FILES FROM THE NET.

Using Netscape go to Protein Data Bank ,

then click on 3Dbrowser and type oxytricha on the TEXT SEARCH field, then click the SEARCH button. The server will return 6 or more matches. Click the first one, the PDB code is 156D.

That is also called the accession number.

Then click on the right EXPLORE button, and then the DOWNLOAD/DISPLAY FILE button. in the FILE FORMAT table click on TEXT (complete with coordinates) then hit the SAVE FULL ENTRY TO DISK button, this will save the pdb file in your computer

with the name 156d.pdb. (NOTE: make a note of the directory in the local disk where the pdb file is saved)

B) BASIC RASMOL COMMANDS

Mouse actions:

Right Mouse = TRANSLATION

Left Mouse = ROTATION

Right Mouse + SHIFT = ROTATION ABOUT Z (screen)

(move mouse left or right)

Left Mouse + SHIFT = ZOOM (Move mouse up or down)

Start the RASMOL program and read the file you just downloaded from the PDB server. Go to the FILE menu and click on OPEN and find the file 156d.pdb.

Open the RASMOL COMMAND LINE at the bottom of the screen.

1) Highlight the Phosphate backbone with a 0.2 Angstrom ribbon.:

backbone 0.2

NOTE: Notice that the quadruplex has a large groove, 2 medium grooves

and a small groove.

2) Highlight the T loop in blue and the G quadruplex core in red

select T*.P (this select all Phosphate atoms on the T)

color blue

backbone 0.2

select G*.P

color red

backbone 0.2

3) Check the stacking of the bases in the T loops:

restrict T* (this will select all the T residues)

Click on the atoms and watch the RASMOL COMMAND LINE window, and

identify T5 and T6 or T17 and T18. Notice the base stacking of T5-T6 and

T17-T18.

4) Analyze quadruplex core:

restrict G* (this will select all the G residues)

wireframe 0.2

Notice the stacking of the 4 layers of Gs

5) Highlight solvent channel through the middle of the quadruplex

select G*.O6 (this selects Oxygen 6 on the G bases)

cpk 0.5

6) Highlight single layer of the quadruplex

restrict G1 or G12 or G16 or G21

Notice the Hoogsteen base pairing. Check out the imperfect hydrogen bonding.

7) Highlight Syn-Syn-Anti-Anti glycosidic conformation.

select G1.O3* or G12.O3* or G16.O3* or G21.O3*

color yellow

cpk 0.3

label

This will highlight the oxygen atom O3* on the sugar. Rotate the molecule

in the Z direction (around an axis perpendicular to the computer screen)

Use Right Mouse + SHIFT until the 4 bases are oriented like this:

G12 G21

G16 G1

Observe the Syn-Syn-Anti-Anti conformation.