User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions
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==Introduction== | ==Introduction== | ||
The [[ribosome]] is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as [http://sandwalk.blogspot.com/2009/10/ribosome-and-central-dogma-of-molecular.html the Central Dogma of Molecular Biology]. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains. The ribosome functions as a complex of two complexes of many proteins and RNAs of substantial length; these two complexes are the small ribosomal subunit and the large ribosomal subunit. | The [[ribosome]] is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as [http://sandwalk.blogspot.com/2009/10/ribosome-and-central-dogma-of-molecular.html the Central Dogma of Molecular Biology]. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains. The ribosome functions as a complex of two complexes of many proteins and RNAs of substantial length; these two complexes are the small ribosomal subunit and the large ribosomal subunit. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked. | ||
In 2000, the large ribosomal subunit from <em>Haloracula marismortui</em> was solved. <em>Haloracula</em> is a [Extremophiles|halophilic]] archaea. | In 2000, the large ribosomal subunit from <em>Haloracula marismortui</em> was solved. <em>Haloracula</em> is a [[Extremophiles|halophilic]] archaea. '''The structure revealed that surprisingly no protein was observed close enough the site of peptide bond synthesis to be be involved in the chemistry of the peptidyl transferase reaction, meaning that RNA was responsible for catalysis and that the large subunit is a ribozyme'''. The structure also revealed the details of the tunnel which the nascent peptide chain would exit the ribosome. | ||
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Realized I will need CCA-puromycin part from 1ffz like I used in my other tours of this subunit so I added that to the unzipped version of [[Image:1s72simplified.PDB.gz|file]] that I have been using and stripped out the waters while I was at it, and then gzipped and uploaded. CCA-puro is chain 5 now. File is uploaded at [[1s72ALPHACplusccapuro.PDB.gz]]. {I verified in PyMol that chain 5 only selects CCA-puromycin, unlike the original way it was from 1ffz where it was chain b and selected another protein form the LSU.) | Realized I will need CCA-puromycin part from 1ffz like I used in my other tours of this subunit so I added that to the unzipped version of [[Image:1s72simplified.PDB.gz|file]] that I have been using and stripped out the waters while I was at it, and then gzipped and uploaded. CCA-puro is chain 5 now. File is uploaded at [[1s72ALPHACplusccapuro.PDB.gz]]. {I verified in PyMol that chain 5 only selects CCA-puromycin, unlike the original way it was from 1ffz where it was chain b and selected another protein form the LSU.) | ||
Then I realized that on addition to CCA-puromycin I need sidechains and bases from a few amino acids and nts near to or interacting with the Yarus analog so I added that to the unzipped version of [[Image:1s72simplified.PDB.gz|file]] that I have been ussing and added back all the atoms from to the two nts that pair with the Yarus analog and 2486 [e.c. #2451) that is close to tetrahedral atom and the sidechains close to the Yarus analog. This file is uploaded at [1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB] and despite the fact it doesn't have a .gz extension, IT IS GZIPPED. I had forgotten at first and uploaded the wrong one the first time. | |||
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==Haloracula Large Ribosomal Subunit Components== | ==Haloracula Large Ribosomal Subunit Components== | ||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72/ | <table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72/6' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Large Ribosomal Subunit''' ([[1s72]]), resolution 2.4Å (<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72/6'>initial scene</scene>). <br> | ||
·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}} ··</center></td></tr></table> | ·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}} ··</center></td></tr></table> | ||
The large subunit of the <em>Haloracula marismortui</em> ribosome sediments at 50S, as do the large subunits of archaea and eubacteria. It is composed of two chains of RNA, a 23S chain (2,922 nucleotides long, 946 kDa) and a 5S chain (122 bases long, 39 kDa). Assembled with the RNA are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa).<ref>PMID:10937989</ref> | The large subunit of the <em>Haloracula marismortui</em> ribosome sediments at 50S, as do the large subunits of archaea and eubacteria. It is composed of two chains of RNA, a 23S chain (2,922 nucleotides long, 946 kDa) and a 5S chain (122 bases long, 39 kDa). Assembled with the RNA are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa).<ref>PMID:10937989</ref> | ||
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:#a small <font color="magenta"> 5S rRNA</font> (122 nucleotides)which forms part of the central protuberance seen in the large subunit. | :#a small <font color="magenta"> 5S rRNA</font> (122 nucleotides)which forms part of the central protuberance seen in the large subunit. | ||
:#a large <font color="#fd0162">23S rRNA</font> (3045 nucleotides) - 2833 of the 3045 nucleotides of the <font color="#fd0162">23S rRNA</font> are seen in the structure. | :#a large <font color="#fd0162">23S rRNA</font> (3045 nucleotides) - 2833 of the 3045 nucleotides of the <font color="#fd0162">23S rRNA</font> are seen in the structure. | ||
===The rRNA domains:=== | |||
The secondary structure map of Haloarcula 23S rRNA (below) clearly shows six large RNA domains extending off a large major loop. (See [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php here] for a detailed secondary structure of <em>Haloarcula marismortui</em> 23S rRNA.)<br> | |||
[[Image:Schematic hmarlsu.jpg|left]] | |||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1s72ALPHACplusccapurowithCERTAINSIDECHAINS.PDB' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Large Ribosomal Subunit''' ([[1s72]]), resolution 2.4Å (<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene>). <br> | |||
·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}} ··</center></td></tr></table> | |||
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomains/3'>The six domains of the large subunit ribosomal RNA and 5S rRNA fit into the monolithic subunit like puzzle pieces</scene> | |||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststartdomain1/3'>Domain I</scene> (<font color = "#6080ff">shown in blue</font>) | |||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain2/5'>Domain II</scene> (<font color = "cyan">shown in cyan</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>) | |||
::*<small>Helix 69 is a portion of Domain IV (See the location in [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php the secondary structure]) 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>) | |||
::*<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. | |||
::*In addition to unliganded subunit, the large subunit structure has been solved with substrate analogs which provides a detailed view of the role <font color="red">domain V</font> plays in the chemistry of peptide bond synthesis. One of the analogs was the <font color="magenta">Yarus analog (CCA-puromycin)</font>, known to inhibit translation because it mimics normal substrate, specifically it resembles an unstable transition state intermediate involving both ends of the tRNAs and amino acid and formed during peptide bond synthesis. One atom in particular corresponds to the carbon of the tetrahedral carbon intermediate<ref>PMID: 10937990</ref>. | |||
:::*The <font color="magenta">Yarus analog</font> is observed to bind in <font color="red">Domain V</font> in the structure. | |||
:::*<font color="#ffc832">Guanosine 2284</font> and <font color="lightblue">Guanosine 2285</font> are base-paired with the <font color="magenta">Yarus analog</font>. | |||
:::*<font color = "red">A2486</font> (E. coli #2451) of <font color = "red">Domain V</font> approaches the critical atom of the <font color="magenta">Yarus analog</font>. | |||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain6/6'>Domain VI</scene> (<font color = "#ae00fe">shown in purple</font>) | |||
:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s725srrns/3'>5S rRNA</scene> (<font color = "#FF00FF">shown in magenta</font>), though a separate molecule, is effectively the seventh RNA domain of the large subunit. | |||
===The proteins:=== | ===The proteins:=== | ||
<table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/ | <table width='400' align='right' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='1s72simplified.PDB.gz' size='540' frame='true' align='right' scene='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Large Ribosomal Subunit''' ([[1s72]]), resolution 2.4Å (<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene>). <br> | ||
·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}} ··</center></td></tr></table> | ·· {{Link Toggle halolsuriborRNA}} ·· {{Link Toggle halolsu23SrRNA}} ·· {{Link Toggle halolsu5SrRNA}} ··<br>·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle BlackWhiteBackground}} ··</center></td></tr></table> | ||
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72extenvsglb/ | :<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72extenvsglb/5'>Globular vs. extended proteins</scene> | ||
:*Proteins are generally globular. However, while about half the proteins seen in the crystal structure of the large ribosomal subunit are globular (<font color="orange">shown as orange</font>), interestingly, '''the other half are extended or have large extended regions''' emanating from globular domains (<font color="cyan">shown as cyan</font>). | :*Proteins are generally globular. However, while about half the proteins seen in the crystal structure of the large ribosomal subunit are globular (<font color="orange">shown as orange</font>), interestingly, '''the other half are extended or have large extended regions''' emanating from globular domains (<font color="cyan">shown as cyan</font>). | ||
:*These extended proteins and regions are reminiscent of the [[Intrinsically Unfolded Proteins (IUP)|intrinsically unfolded proteins]] that play roles in many other processes. | :*These extended proteins and regions are reminiscent of the [[Intrinsically Unfolded Proteins (IUP)|intrinsically unfolded proteins]] that play roles in many other processes. | ||
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/4examples/ | :<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/4examples/9'>Particular examples of globular vs. extended proteins</scene> | ||
:Zooming in to see some examples in more detail: | :Zooming in to see some examples in more detail: | ||
:*L2, L15, and L39e illustrate proteins with extended regions. | :*L2, L15, and L39e illustrate proteins with extended regions. | ||
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:*L39e is extended over its entire length. | :*L39e is extended over its entire length. | ||
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/Extensionpenetrate/ | :<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/Extensionpenetrate/3'>Extensions penetrate into the subunit interior</scene> | ||
:*View of L2, L15, L39e and L7ae again but with the RNA backbone shown. The extended regions are <font color="cyan">again highlighted in cyan</font>. | :*View of L2, L15, L39e and L7ae again but with the RNA backbone shown. The extended regions are <font color="cyan">again highlighted in cyan</font>. | ||
:*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements. | :*Using the mouse to spin around the structure clearly shows that the extended proteins penetrate into the interior to fill gaps between RNA secondary structure elements. | ||
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===Polypeptide Exit Tunnel=== | ===Polypeptide Exit Tunnel=== | ||
*Polypeptide Exit Tunnel | *Polypeptide Exit Tunnel | ||
As the nascent chain grows, it advances into a tunnel that passes through the large subunit, called the polypeptide exit tunnel. | |||
==Structures== | ==Structures== | ||
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==See Also== | ==See Also== | ||
* [[Ribosome]] | * [[Ribosome]] | ||
* Small Ribosomal Subunit | |||
* [[Nobel Prizes for 3D Molecular Structure]] | * [[Nobel Prizes for 3D Molecular Structure]] | ||
* [[Extremophiles]] | * [[Extremophiles]] | ||
