3D MODEL
The construction of a 3 D model structure of the mammalian mitochondrial small ribosomal subunit is being undertaken using the E.coli small ribosomal subunit as a homologue.  The various mitoribosomal proteins are being located within this model, based on published coordinates of their homologues.  Earlier versions of the models, including one developed by Wes Faunce will appear on this page in the future, along with models being developed with Robert Stiff.  As another starting point, Tom O'Brien, working with Russell Salfi, is modeling the bovine small mitoribosomal subunit using the published data from

Dr. Harry Noller
University of California
Santa Cruz, CA 95064

As available at the RiboWeb page: 

 http://smi-web.stanford.edu/projects/helix/ribo3dmodels/noller-m.html
            For two freeware programs used to render the 3d models found here, please go to the appropriate web site bellow and down-load the program for your machine.  A special thanks to the excellent programmers:
Craig Kloeden, author of the Mac version Rotate, http://raru.adelaide.edu.au/craig
and
Marijke van Gans, author of the PC version Rotate; send email to marijke@silicon-alley.com 

    
 
For the Mac, Rotater: http://raru.adelaide.edu.au/rotater   
For the PC, Rotate: http://www.silicon-alley.com/cat/rotate.html      
 
Disclamer:        
All programs, files, renderings, and information given here is done so as gratis and carry 
NO guarantee/guarantees of usefulness, accuracy, compatibility, safety, and/or other 
stated or implied benefit.
Page down to see several animated images! 
         

A recent version of the modeled regions (by Harry Noller) of E. coli 16S RNA
 depicting the XYZ coordinates of the phosphates in the RNA

     

  

     

Here are the E. coli 30S subunit proteins represented as spheres
("Neutron map" from Peter Moore's lab)
   

  

     

The RNA helical regions represented as cylinders, single strand loop
regions as polygon caps
   
 
       

The cylinders and spheres together
   
 

 

 
 
 
 
 

In order to view these files in the Rotater and Rotate programs go to

http://www.med.ufl.edu/biochem/tobrien/files.rot/    by entering this address in
your browser and press <ENTER> ,  then  follow the instructions below. 

3D Renderings:
 
using your web browser open the following   *.rot  files and then save them at text.
Once they have been saved to disk or hard drive they can be opened using either
the Mac: Rotater or PC: Rotate programs.
 
noller_m.rot 
  The rendering of the H. Noller data giving the tertiary structure of the phosphate chain
  in the e.coli small ribosomal unit.
 
cylcap.rot
  The rendering of the RNA tertiary with the double helix regions represented as stacked
  circles, and the single strand loops as 3 stacked polygons.
 
nolcyl.rot
  The rendering of phosphate chain in the RNA overlaid with the cylinders and caps.
 
spheres.rot
  The rendering of the proteins  S3  through  S21  represented as spheres.
 
nolsph.rot
  The rendering of the phosphate chain in the RNA with the protein spheres.
 
cylsph.rot 
  The rendering of the RNA cylinder and cap representations with the protein spheres.
TI-83 Programs:
 
To generate the R^3, XYZ points for the stacked circles (cylinders), caps, and spheres
in theabove renderings a Texas Instruments TI-83 graphing calculator was used
 

http://www.ti.com/calc/docs/83.htm
  along with the Texas Instruments TI - GRAPH LINK ,which allows the calculator to be interfaced with a desktop computer, Mac or PC. Once the coordinates were stored in the TI-83 lists L3, L4, and L5 the data was then transfered to a desktop computer and incorporated in a text file that
the Rotater and Rotate programs use to generate the renderings.
  

http://www.ti.com/calc/docs/link.htm
  Here are the TI-83 programs, once you have save them to disk or hard drive use the TI-83 GRAPH LINK program 
http://www.ti.com/calc/docs/link83.htm
  <Tools> to UUDecode the text files into *.83p programs that can be linked and transfered to your TI-83 using the TI-GRAPH LINK.
The TI-83 programs are found in

http://www.med.ufl.edu/biochem/tobrien/ti83prgms/

you will have to enter this address in your browser and press <ENTER>
click on the program you wish to save, and then save the UUE as text
to floppy or hard drive, once this is done UUE decode the saved file
with the TI-83 graph link program.
 


TI-83.p Programs:
 
MPCYL.TXT
  This program finds the midpoint between the initial and terminal base pairs
  in  helical RNA region, these midpoints are then used to construct a
  direction vector that is orthogonal to the stacked circles and passes through
  their centers.  Used in CYLNDR.83p.
 
CYLNDR.TXT
  This program generates 21 R^3 points per circle, one circle for each of the base
  pairs in the RNA double helix region represented.
 
MPCAP.TXT
  This program generates the midpoints for the initial and terminal base pairs
  in a  helical RNA region when the data for the caps is being generated.
  Used in CAPS.83p.
 
CAPS.TXT
  This program generates the R^3 points used to render the 3 stracked regular
  polygons that the represent the single strand regions that loop at the ends of RNA helices.
 
SPHERE.TXT
  This program generates 100 random points on a sphere with radius and
  center that represent the proteins  S2 - S21 in the "neutron map" from the Peter Moore lab.
 
Note:  Rotater and Rotate files are text files with  < X   Y   Z   connect, color  > data for
            each line in the read file.  With not too much experience you can create your
            own Rotater and Rotate files and render your own molecular models.