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

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| <applet load='Paromomycinfrom2j00.pdb.gz' size='390' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/Paromomycin/1' />
| <applet load='Paromomycinfrom2j00.pdb.gz' size='390' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/Paromomycin/1' />
||
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|<table width='410' align='left' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='2j01and2j00andrestofAsitetRNAalphac.pdb.gz' size='410' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Paromomycin bound to the ribosome''' ([[2j01]] and [[2j00]), resolution 2.8&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1'>initial scene</scene>). <br>
|<table width='410' align='left' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='2j01and2j00andrestofAsitetRNAalphac.pdb.gz' size='410' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''REPLACE WITH PAROMOMYCN BOUND TO SMALL SUBUNIT'''<br>'''Paromomycin bound to the ribosome''' ([[2j01]] and [[2j00]]), resolution 2.8&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/1'>initial scene</scene>). <br>
·· {{Link Toggle halolsuriborRNAb}} ·· {{Link Toggle halolsu23SrRNAb}} ·· {{Link Toggle halolsu5SrRNAb}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}}  ··</center></td></tr></table>
·· {{Link Toggle halolsuriborRNAb}} ·· {{Link Toggle halolsu23SrRNAb}} ·· {{Link Toggle halolsu5SrRNAb}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}}  ··</center></td></tr></table>
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<table width='550' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='2j01and2j00andrestofAsitetRNAalphac.pdb.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Paromomycin bound to the ribosome''' ([[2j01]] and [[2j00]]), resolution 2.8&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1'>initial scene</scene>). <br>
<table width='550' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='2j01and2j00andrestofAsitetRNAalphac.pdb.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Paromomycin bound to the ribosome''' ([[2j01]] and [[2j00]]), resolution 2.8&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithpar/1'>initial scene</scene>). <br>
·· {{Link Toggle 70SribotRNAs}} ·· {{Link Toggle 70SribomRNA}} ·· {{Link Toggle 70SriborRNA}} ·· {{Link Toggle 70SriboProtein}} ··<br>
·· {{Link Toggle 70SselmerribotRNAs}} ·· {{Link Toggle 70SselmerribomRNA}} ·· {{Link Toggle 70SriborRNA}} ·· {{Link Toggle 70SriboProtein}} ··<br>
·· {{Link Toggle 70SselmerriboAsitetRNA}} ·· {{Link Toggle 70SriboPsitetRNA}} ·· {{Link Toggle 70SriboEsitetRNA}} ·· <br>
·· {{Link Toggle 70SselmerriboAsitetRNA}} ·· {{Link Toggle 70SselmerriboPsitetRNA}} ·· {{Link Toggle 70SselmerriboEsitetRNA}} ·· <br>
·· {{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/70swithpar/1'>TextToBeDisplayed</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>.


Add the e. coli 70S that has two molecules bound
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];-->
 
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]]




<ref>PMID: 12765838</ref>
<ref>PMID: 12765838</ref>
<ref>PMID: 12464183</ref>
<ref>PMID: 11340196</ref>
<ref>PMID: 11014183</ref>
<ref>PMID: 17660832</ref>
<ref>PMID: 17116475</ref>
<ref>PMID: 16569869</ref>
<ref>PMID: 12517339</ref>
<ref>PMID: 15491801</ref>


==References==
==References==
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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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