Ribosomal A Site Binding Paromomycin: A Morph

From Proteopedia

This page displays an oligo-RNA containing a minimal decoding A site of the small subunit of the bacterial ribosome. The model without PAR is an oligo-RNA (from 3bnl) which has cobalt hexammine (not shown) bound in its larger groove. The model with PAR is complexed to paromomycin, an aminoglycoside antibiotic (shown spacefilling) that blocks translation (from 1j7t). The morph shows the transition between these two states, prepared in collaboration with Moran Shalev (Technion, Haifa, Israel).

The initial scene is without PAR. Toggle Quality ON for improved displays. Be sure to rotate the morphs with the mouse to watch them from various perspectives.

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• Without PAR ().

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• . Sometimes you have to scroll the browser a little to start the animation.

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You can popup any of the above scenes. When popping up the morph, toggle quality OFF. It has little effect on quality in a large Jmol, but it does slow the morph animation considerably.

Technical: Morphing

The morph adds, to the two empirical models, 8 interpolated frames generated by the Yale Morph Server (see Morphs). To the 10 models of the morph was added an 11th model containing only PAR, for purposes of showing it as a translucent "background" during the morph animation. The resulting 11-model PDB file was uploaded as Image:Moran asite par morph.pdb. Below is the script for the morph. In the SAT, the uploaded PDB file was loaded, then the Jmol Console was opened, and the script below was pasted in and run (with the "load" command commented out). The morph should then animate with the desired appearance in the SAT, namely, model 1.11 (translucent PAR) should be the constant background model, and it should not be included in the animation as the last frame (without RNA). The result was then saved as a scene, leaving "animate" unchecked. (The "animate" option is using a command, 'anim on', that resets the frame range to all frames. I have requested that is use instead 'frame play' which does not.)

If you use the SAT to edit the representation or coloring of the morph, you will need to enter the command "frame play" in the Jmol Console just before saving the scene, leaving "animate" unchecked.

The script below was developed in the Jmol application (Jmol.jar). The script will play offline if you put the PDB file, Jmol.jar, and the script in a file named 1.spt all in one directory, then double click Jmol.jar, then open the Script Console (right click on the black Jmol, then click Console on Jmol's menu), and enter (in the bottom box) "script 1.spt".

# The Yale Morph Server numbered the models 0-10. However, model/frame 0 has
# a special meaning in Jmol, namely, all models. In order to reduce confusion,
# I renumbered the models (by hand editing) 1-11.

zap;
color background white;
set antialiasdisplay on; # smoother rendering, speed penalty seems acceptable.

load moran_asite_par_morph.pdb;
spacefill off;
wireframe off;

# don't make par wireframe -- it shows thru the translucent spacefill.
select nucleic;
wireframe 0.1;

select par; # selects it in both the penultimate and ultimate models.
spacefill;

# We want par to appear translucent except in the last frame of the animation,
# where it is bound and should be opaque.
# Method: coordinates for par will be in two models: the next to last model
# (together with RNA), and the last model (by itself).
# par alone is in model 11 = frame 1.11.
# We'll make that translucent and set it as a background model.
# model 10 = frame 1.10 contains the last conformation of RNA plus par.
# We'll make that par opaque. It will show (covering up the translucent par)
# only in the last frame of the animation.

select par and model=11;
color translucent -1;
set backgroundmodel 1.11;

# model 10 is the last model with nucleic, and it also has par.
select par and model=10;
color opaque;

anim mode palindrome;

#frame 1.11 is the ligand PAR by itself.
# set frame range for anim
frame 1.1 1.10; # exclude frame 1.11 from the anim.
#frame range 1.1 1.10; #alternative syntax

# N.B. 'anim on' resets frame range! 'frame play' does not.
frame play;