User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin: Difference between revisions

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·· {{Link Toggle 70SriboLSU}} ·· {{Link Toggle 70SriboSSU}} ·· {{Link Toggle BlackWhiteBackground}}  ·· <br></center></td></tr></table>
·· {{Link Toggle 70SriboLSU}} ·· {{Link Toggle 70SriboSSU}} ·· {{Link Toggle BlackWhiteBackground}}  ·· <br></center></td></tr></table>


<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/1'>In the Thermus 70S paromomycin is observed binding to the penultimate helix of the small subunit (helix 44) at the decoding center.</scene>
The 70S is so large that the small paromomycin molecule is not readily obvious, and so <scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/6'>here the view zooms in and paromomycin is highlighted by making the ribosome partially translucent</scene>.


<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/2'>In the Thermus 70S paromomycin is observed binding to the penultimate helix of the small subunit (helix 44) at the decoding center.</scene> WHY IS 5S (:b and 1.1) SHOWING NOT TRANSPARENT!?!?! WASN"T THAT I USED ' color [x777777]' BECAUSE WENT BACK TO USING SAT AND ALTHOUGH IT LOOKS FINE WHEN LOADED IN SAT, WHEN TRIGGERED FROM GREEN LINK IT IS NOT TRANSPARENT?!?!??!? MAybe change all to transparent again and switch back par? I doubt that will help since I used all to change at first anyway, but could try.)
Returning to  <scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1'>the initial scene of the full ribosome</scene> now aware of the locale where paromomycinin is bound, it is clear that in the Thermus 70S paromomycin is observed binding to the penultimate helix of the small subunit (helix 44) at the decoding center where the anticodon stem-loop of the <font color = 'pink'>'''A-site tRNA'''</font> contacts the mRNA (shown as yellow). 
<!--After much work, finally got 5S to go transparent by turning off cartoon and making it trace. Others seemed fine with cartoon. See
<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/3'>TextToBeDisplayed</scene>
IN FACT LATER IT SEEMED I HAD TO PASTE SPECIAL LINE IN COMMAND BEFORE SAVING EACH TIME TO GET 5S TO SAVE TRANSPARENT. SPECIAL LINE OF CODE TO PASTE:select 1.1 and :b; cartoon off; trace 1.0; color [x888888];-->


Add the e. coli 70S that has two molecules bound
NEED TO DO STILL: Add the e. coli 70S that has two molecules bound


==About these Structure==
==About these Structure==
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==Related Structures==
==Related Structures==
*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit|Haloarcula Large Ribosomal Subunit]]
*[[Large Ribosomal Subunit of Haloarcula|Haloarcula Large Ribosomal Subunit]]
*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]]
*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]]


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<ref group="xtra">PMID:15491801</ref>
<ref group="xtra">PMID:15491801</ref>
<references group="xtra"/>  
<references group="xtra"/>  
*[http://www.youtube.com/watch?v=E6wXlpkQVww Lecture by Venki Ramakrishnan in 2004 entitled The Ribosome: The Cell's Protein-Synthesizing Machine and How Antibiotics Disrupt It] - posted on Brookhaven National Laboratory's Channel
*[http://www.drugbank.ca/drugs/DB01421 Paramomycin at the DrugBank database]
*[http://www.drugbank.ca/drugs/DB01421 Paramomycin at the DrugBank database]
*[http://en.wikipedia.org/wiki/Paromomycin_sulfate Paromomycin sulfate at Wikipedia]
*[http://en.wikipedia.org/wiki/Paromomycin_sulfate Paromomycin sulfate at Wikipedia]
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