User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions
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:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain3/6'>Domain III</scene> (<font color = "yellow">'''shown in yellow'''</font>) | :*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain3/6'>Domain III</scene> (<font color = "yellow">'''shown in yellow'''</font>) | ||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain4/7'>Domain IV</scene> (<font color = "#00FF00">'''shown in green'''</font>) | :*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain4/7'>Domain IV</scene> (<font color = "#00FF00">'''shown in green'''</font>) | ||
::*<small>Helix 69 is a portion of Domain IV | ::*<small>Helix 69 is a portion of Domain IV <ref>Helix 69 is shown clearly in Domain IV in [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php a detailed secondary structure of Haloarcula marismortui 23S rRNA]</ref>and is part of one of the important conserved intersubunit bridges of the ribosome (b2a), although '''it is not visible in this structure'''. (The 13-nt stem-loop not seen would connect the highlighted spheres <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain4h69/2'>here</scene>.) See the [[ribosome]] to see a structure where helix 69 is observed in the solved structure, extending from the large subunit under the A- and P- site tRNAs in the 70S ribosome and contacting the tRNAs and the small subunit decoding center. Helix 69 plays a roles in initiation, termination, and disassembly of the ribosome post-termination</small><ref>PMID: 17996252</ref><ref>PMID: 19007789</ref><ref>PMID: 16973438</ref>. | ||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5/6'>Domain V</scene> (<font color = "red">'''shown in red'''</font>) | :*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5/6'>Domain V</scene> (<font color = "red">'''shown in red'''</font>) | ||
::*<font color="red">'''Domain V'''</font> lies at the core of the subunit. It is known to be intimately associated with the peptidyl transferase reaction that occurs during translation. This is further explored further [[#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|below]]. | ::*<font color="red">'''Domain V'''</font> lies at the core of the subunit. It is known to be intimately associated with the peptidyl transferase reaction that occurs during translation. This is further explored further [[#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|below]]. | ||
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==Additional Literature== | ==Additional Literature== | ||
<ref group="xtra">PMID:19222865</ref><ref group="xtra">PMID: 18292779</ref><ref group="xtra">PMID: 19962317</ref><ref group="xtra">PMID: 19838167</ref><ref group="xtra">PMID: 11297922</ref><ref group="xtra">PMID: 20562215</ref><references group="xtra"/> | <ref group="xtra">PMID:19222865</ref><ref group="xtra">PMID: 18292779</ref><ref group="xtra">PMID: 19962317</ref><ref group="xtra">PMID: 19838167</ref><ref group="xtra">PMID: 11297922</ref><ref group="xtra">PMID: 20562215</ref><ref group="xtra">PMID: 23771137</ref><references group="xtra"/> | ||
==External Resources== | ==External Resources== | ||
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*[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ The Nobel Prize in Chemistry 2009 page at The Official Web Site of the Nobel Prize] | *[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ The Nobel Prize in Chemistry 2009 page at The Official Web Site of the Nobel Prize] | ||
*[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb10_1.html Ribosome: October 2000 Molecule of the Month] as part of the series of tutorials that are at [http://www.pdb.org/pdb/home/home.do the RCSB Protein Data Bank] and written by [[User:David_S._Goodsell|David Goodsell]] | *[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb10_1.html Ribosome: October 2000 Molecule of the Month] as part of the series of tutorials that are at [http://www.pdb.org/pdb/home/home.do the RCSB Protein Data Bank] and written by [[User:David_S._Goodsell|David Goodsell]] | ||
* [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php A detailed secondary structure of Haloarcula marismortui 23S rRNA] at the http://people.biochem.umass.edu/fournierlab/3dmodmap/main.php 3D Ribosomal Modifications Map Database] | *[http://apollo.chemistry.gatech.edu/RiboVision/ RiboVision] - a nice way to explore the representative structures with the secondary structures of the RNA side-by-side with the 3D structure, from from Georgia Institute of Technology and NASA. | ||
*The people behind [http://apollo.chemistry.gatech.edu/RiboVision/ RiboVision] have determined a [http://nar.oxfordjournals.org/content/41/15/7522.short?rss=1 revised secondary structure for two of the rRNAs] based on the 3D structures and it is described in [http://www.ncbi.nlm.nih.gov/pubmed/23771137?dopt=Abstract their paper]<ref group="xtra">PMID: 23771137</ref>. | |||
* [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php A detailed secondary structure of Haloarcula marismortui 23S rRNA] at the [http://people.biochem.umass.edu/fournierlab/3dmodmap/main.php 3D Ribosomal Modifications Map Database] | |||
