User:Wayne Decatur/Sandbox Thermus 70S With Paromomycin

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Current revision (17:23, 14 May 2010) (edit) (undo)
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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>
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The 70S is so large that the small paromomycin that is bound is not readily obvious, and so <scene name='User:Wayne_Decatur/Sandbox_Thermus_70S_With_Paromomycin/70swithparbest/6'>here the view zooms in and highlights paromomycin by making the ribosome partially translucent</scene>.
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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>.
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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 tRNA contacts the mRNA.
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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
<!--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>
<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];-->
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];-->
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Add the e. coli 70S that has two molecules bound
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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==
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*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit|Haloarcula Large Ribosomal Subunit]]
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*[[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"/>
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*[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]

Current revision

Ribosome interactions with Paromomycin


Contents

Mechanism of action

Drag the structure with the mouse to rotate
 
Drag the structure with the mouse to rotate
REPLACE WITH PAROMOMYCN BOUND TO SMALL SUBUNIT
Paromomycin bound to the ribosome (2j01 and 2j00), resolution 2.8Å ().
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·· ·· ··

NEED TO DO STILL: SSU alone with PAR


Ramakrishnan one with Par

 
Drag the structure with the mouse to rotate
Paromomycin bound to the ribosome (2j01 and 2j00), resolution 2.8Å ().

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·· ·· ·· ··

The 70S is so large that the small paromomycin molecule is not readily obvious, and so .

Returning to 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 A-site tRNA contacts the mRNA (shown as yellow).

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

About these Structure

2j00 is a 25 chains structure of sequences from Escherichia coli and Thermus thermophilus. Full crystallographic information is available from OCA.

2j01 is a 31 chains structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA. Versions of 2j00 and 2j01 optimized for use online as described here are used on this page. You may wish to examine the ADD LINK basics of the subunit.

Reference for the Structures

  • Selmer M, Dunham CM, Murphy FV 4th, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science. 2006 Sep 29;313(5795):1935-42. Epub 2006 Sep 7. PMID:16959973

Related Structures


[1]

References

  1. ↑ Ogle JM, Carter AP, Ramakrishnan V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci. 2003 May;28(5):259-66. PMID:12765838

Additional Literature and Resources

  • Auerbach T, Bashan A, Yonath A. Ribosomal antibiotics: structural basis for resistance, synergism and selectivity. Trends Biotechnol. 2004 Nov;22(11):570-6. PMID:15491801 doi:10.1016/j.tibtech.2004.09.006

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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