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[[Image:SSU front and LSU front side by side white backgroundSMALL.jpg|middle|500px]]<br>
<StructureSection load='4v42' size='450' side='right' scene='User:Wayne_Decatur/SandboxRibosome/Bothmodels6/1' caption='The Ribosome ([[4v42]])'>
 
__TOC__
 
[[Image:Screen capture of 70S white background spacefill tRNAS.jpg|left|300px]]<br />
 
 
 
'''The Ribosome'''<br>
'''The protein synthesis machine of cells''' <br>
'''shown with the 3 transfer RNAs and messenger RNA bound.'''
 
 
 
 
==Introduction==
==Introduction==
<table width='550' align='right' cellpadding='5'><tr><td rowspan='2'>&nbsp;</td><td bgcolor='#eeeeee'><applet load='1jgo1giy.gz.pdb' size='540' frame='true' align='right' scene='User:Wayne_Decatur/SandboxRibosome/Bothmodels6/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''The Ribosome''' ([[1jgo]] and [[1giy]]), resolution 5.5&Aring; (<scene name='User:Wayne_Decatur/SandboxRibosome/Bothmodels6/1'>initial scene</scene>). <br>
·· {{Link Toggle 70SribotRNAs}} ·· {{Link Toggle 70SribomRNA}} ·· {{Link Toggle 70SriborRNA}} ·· {{Link Toggle 70SriboProtein}} ··<br>
·· {{Link Toggle 70SriboAsitetRNA}} ·· {{Link Toggle 70SriboPsitetRNA}} ·· {{Link Toggle 70SriboEsitetRNA}} ·· <br>
·· {{Link Toggle 70SriboLSU}} ·· {{Link Toggle 70SriboSSU}} ·· {{Link Toggle BlackWhiteBackground}}  ·· <br></center></td></tr></table>
The [http://en.wikipedia.org/wiki/ribosome 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 [http://en.wikipedia.org/wiki/ribosome 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.
*'''30S ribosome''' - prokaryote small subunit
*'''40S ribosome''' - eukaryote small subunit
*'''pre-40S ribosome''' - eukaryote small subunit with associated assembly factors
*'''43S ribosome''' - eukaryote preinitiation small subunit containing eIF3, eIF1 and eIF1A
*'''48S ribosome''' - eukaryote small subunit initiation complex containing Met-tRNA
*'''50S ribosome''' - prokaryote large subunit
*'''60S ribosome''' - eukaryote large subunit
*'''pre-60S ribosome''' - eukaryote nucleolar large subunit with associated assembly factors
*'''70S ribosome''' - prokaryote full ribosome containing small and large subunits
*'''80S ribosome''' - eukaryote full ribosome containing small and large subunits
*'''90S pre-ribosome''' - eukaryote an early biogenesis ribosome intermediate containing assembly factors and small nucleolar RNAs.
*'''100S ribosome''' - a dimer of prokaryote full ribosomes


==Nobel Prize Winners and Other Contributors==
==Nobel Prize Winners and Other Contributors==
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==Ribosome Components==
==Ribosome Components==
<br>
·· {{Link Toggle 70SribotRNAs}} ·· {{Link Toggle 70SribomRNA}} ·· {{Link Toggle 70SriborRNA}} ·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle 70SriboAsitetRNA}} ·· {{Link Toggle 70SriboPsitetRNA}} ·· {{Link Toggle 70SriboEsitetRNA}} ·· {{Link Toggle 70SriboLSU}} ·· {{Link Toggle 70SriboSSU}} ·· {{Link Toggle BlackWhiteBackground}}  ··
The small subunit of the prokaryotic ribosome sediments at 30S<ref>[http://en.wikipedia.org/wiki/Svedberg Svedberg unit] in Wikipedia</ref>. It is composed of a 16S chain of RNA about 1,500 bases long (~500 kDa), plus about 20 protein chains. The proteins in the first small subunit determined range from about 3 kDa to 29 kDa.
The small subunit of the prokaryotic ribosome sediments at 30S<ref>[http://en.wikipedia.org/wiki/Svedberg Svedberg unit] in Wikipedia</ref>. It is composed of a 16S chain of RNA about 1,500 bases long (~500 kDa), plus about 20 protein chains. The proteins in the first small subunit determined range from about 3 kDa to 29 kDa.


The large subunit of the prokaryotic ribosome sediments at 50S. It is composed of two chains of RNA, a 23S chain (~3000 bases long, 946 kDa) and a 5S chain (~120 bases long, 39 kDa). Assembled with the RNA are about 30 protein chains. The proteins in the first large subunit determined range from 6 kDa to 37 kDa.
The large subunit of the prokaryotic ribosome sediments at 50S. It is composed of two chains of RNA, a 23S chain (~3000 bases long, 946 kDa) and a 5S chain (~120 bases long, 39 kDa). Assembled with the RNA are about 30 protein chains. The proteins in the first large subunit determined range from 6 kDa to 37 kDa.  See also [[Large Ribosomal Subunit of Haloarcula]].  The large subunit contains several [[Kink-turn motif]]s.
 
The ''mitochindrial ribosome'' or '''mitoribosome''' is smaller than the the cytoplasmic ribosome with a small subunit which sediments at 28S and a large subunit which sediments at 39S.  The whole mitoribosome sediments at 55S.


Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain.
Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain.
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*<b>Yonath lab original atomic-resolution structures</b><ref>PMID: 11007480</ref><ref>PMID: 11733066</ref>: <em>Thermus thermophilus</em> small ribosomal subunit - [[1fka]], improved in [[1i94]], [[1i95]], [[1i96]], and [[1i97]]. <em>Thermus thermophilus</em> is a [[Extremophiles|thermophilic]] eubacteria. <em>Deinococcus radiodurans</em> large ribosomal subunit - [[1nkw]], later refined to give [[2zjr]]. <em>Deinococcus radiodurans</em> is a mesophilic eubacteria.<br>
*<b>Yonath lab original atomic-resolution structures</b><ref>PMID: 11007480</ref><ref>PMID: 11733066</ref>: <em>Thermus thermophilus</em> small ribosomal subunit - [[1fka]], improved in [[1i94]], [[1i95]], [[1i96]], and [[1i97]]. <em>Thermus thermophilus</em> is a [[Extremophiles|thermophilic]] eubacteria. <em>Deinococcus radiodurans</em> large ribosomal subunit - [[1nkw]], later refined to give [[2zjr]]. <em>Deinococcus radiodurans</em> is a mesophilic eubacteria.<br>


*<b>Ramakrishnan lab original atomic-resolution structures</b><ref>PMID: 11014182</ref><ref>PMID: 11014183</ref>: <em>Thermus thermophilus</em> small ribosomal subunit -[[1fjf]] which was later refined to [[1j5e]]. Related: in complex with the antibiotics streptomycin, spectinomycin, and paromomycin in [[1fjg]]; in complex with tetracycline in [[1hnw]], pactamycin in [[1hnx]], hygromycin B in [[1hnz]].
*<b>Ramakrishnan lab original atomic-resolution structures</b><ref>PMID: 11014182</ref><ref>PMID: 11014183</ref>: <em>Thermus thermophilus</em> small ribosomal subunit in [[1j5e]]. Related: in complex with the antibiotics streptomycin, spectinomycin, and paromomycin in [[1fjg]]; in complex with tetracycline in [[1hnw]], pactamycin in [[1hnx]], hygromycin B in [[1hnz]].
The <em>Thermus thermophilus</em> small ribosomal subunit is composed of a 16S chain of RNA about 1,522 bases long (494 kDa), plus 20 protein chains (S2-S20, THX). The protein chains range from 26 (THX, 3 kDa) to 256 amino acids (S2, 29 kDa).  
The <em>Thermus thermophilus</em> small ribosomal subunit is composed of a 16S chain of RNA about 1,522 bases long (494 kDa), plus 20 protein chains (S2-S20, THX). The protein chains range from 26 (THX, 3 kDa) to 256 amino acids (S2, 29 kDa).  


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*[[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] as solved by the Steitz & Moore labs.<br>
*[[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] as solved by the Steitz & Moore labs.<br>
*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]]<br>
*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]]<br>
*[[Large Ribosomal Subunit of Haloarcula]]<br />
*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|Azithromycin bound to the Large Ribosomal Subunit of Haloarcula marismortui]]<br>
*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|Azithromycin bound to the Large Ribosomal Subunit of Haloarcula marismortui]]<br>
*[[Azithromycin]]<br />
*[[Clarithromycin]]<br />
*[[Doxycycline]]<br />
*[[40S rRNA and proteins and P/E tRNA for eukaryotic ribosome]]<br />
*[[Ribosomal A Site Binding Paromomycin: A Morph]]<br />
*[[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]]<br />
*[[Ribosome structure]]<br />
*[[Ribosome structure (Spanish)]]<br />
*[[Ribosome (Czech)]]<br />


==Additional Ribosome Structures==
==Ribosome 3D structures==
<b>Several other ribosome structures have now been published, and here are just a few of these entries in Proteopedia (with apologies to the authors of those not yet listed):<br></b>
 
*[[2j00]] and [[2j01]] are the subunits of the 70S ribosome structure from the Ramakrishnan lab; the aminoglycoside antibiotic paromomycin is present as well. [[2j02]] and [[2j02]] form another molecule described in the accompanying report.<br>
[[Ribosome 3D structures]]
*[[1gix]] and [[1giy]] are the subunits of the 70S ribosome structure determined by the Noller lab, the first for the 70S at near-atomic resolution; more of the mRNA chain is seen in [[1jgo]].<br>
*[[2i2u]] and [[2i2v]] are the subunits of the <em>E. coli</em> ribosome at 3.2 &Aring; as solved by the Cate lab. [[2i2t]] and [[2i2p]] are related structures.<br>
*[[2gya]] and [[2gy9]] are the subunits of a complete <em>E. coli</em> ribosome as determined by cryo-EM by Joachim Frank's lab.<br>
*[[3u5b]], [[3u5c]], [[3u5d]], [[3u5e]], [[3u5f]], [[3u5g]], [[3u5h]], and [[3u5i]]  are the subunits of the eukaryotic 80S ribosome of the baker's yeast ''Saccharomyces cerevisiae'' at a glorious 3.0 &Aring; — including nearly all ribosomal RNA bases and protein side chains.<br>
*[[1ibk]] is paromomycin bound to the small subunit.<br>
*[[1ibm]] is the small subunit with an mRNA analog bound and an anticodon stem loop bound to the A site.<br>
*Small subunit bound to near-cognate tRNA anticodon stem-loop: [[1n32]], [[1n33]], [[1n34]], [[1n36]]<br>
*[[2ow8]] and [[1vsa]] are the subunits of a 70S-tRNA-mRNA complex from the Noller lab.<br>
*Macrolide, lincosamide, streptogramin B, and ketolide antibiotics bound to the large subunit, which impacts mechanisms of drug resistance:[[1yi2]], [[1yj2]], [[1yit]], [[1yhq]], [[1yjn]], [[1yij]], and [[1yj9]] <br>
*Refined ''H. marismortui'' 50S ribosomal subunit and its interaction with anisomycin and mutations outside the binding site that make it drug-resistant: [[3cc2]], [[3cc4]], [[3cc7]], [[3cce]], [[3ccj]], [[3ccl]], [[3ccm]], [[3ccq]], [[3ccr]]  [[3ccs]], [[3ccu]], [[3ccv]] and [[3cd6]]   
*Chloramphenicol bound to the ''H. marismortui'' 50S ribosomal subunit: [[1nji]]<br>
*Chloramphenicol bound to the ''D. radiodurans'' 50S ribosomal subunit: [[1k01]]<br>
*The antibiotic linezolid (example of the first new class of antibiotics to enter into clinical usage within the past 30 years) bound to the large ribosomal subunit of ''D. radiodurans'': [[3dll]]<br>
*Thiopeptide antibiotics bound to the large ribosomal subunit of ''D. radiodurans'': [[2zjp]], [[2zjq]],and [[3cf5]]<br>
*Macrolide antibiotics bound to the large ribosomal subunit of ''D. radiodurans'': [[2o43]], [[2o44]], and [[2o45]]<br>
*Ribosome Binding Domain of the Trigger Factor in complex with the large ribosomal subunit of ''D. radiodurans'': [[2d3o]] and [[2aar]]<br>
*Initiation factor 1 bound to the small subunit: [[1hr0]]<br>
* [[4abr]] and [[4abs]] show the ''Thermus thermophilus'' 50S ribosomal subunit bound by a tmRNA fragment, SmpB and elongation factor Tu at 3.2 &Aring; as solved by the lab of V. Ramakrishnan.
*70S interaction with the Shine-Dalgarno sequence: [[2qnh]] and [[1vsp]].<br>
*Ribosome Recycling Factor bound to the 70S Ribosome: [[2v46]], [[2v47]], [[2v48]], and [[2v49]] <br>
*[[2e5l]] shows the small subunit with an mRNA mimic bound and the Shine-Dalgarno and anti-Shine-Dalgarno sequences interacting.<br>
*70S ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon: [[2b64]] and [[2b66]]<br>
*Structures of the 30S bound with anticodon stem-loops from tRNAs that facilitate frame-shifting: [[2uxb]], [[2uxc]], and [[2uxd]]<br>
*70S Ribosome in complex with mRNA, paromomycin, acylated A- And P-Site tRNAs, and E-Site tRNA: [[2wdg]], [[2wdh]], [[2wdi]], [[2wdj]], [[2wdk]], [[2wdl]], [[2wdm]], and [[2wdn]]<br>
* ''E. coli'' 70S ribosome in complex with paramomycin and ribosome recycling factor: [[2qal]], [[2qam]], [[2qan]], [[2qao]], [[2qb9]], [[2qba]], [[2qbb]], [[2qbc]], [[2qbd]], [[2qbe]], [[2qbf]], [[2qbg]], [[2qbh]], [[2qbi]], [[2qbj]], [[2qbk]], [[2z4k]], [[2z4l]], [[2z4m]], and [[2z4n]].<br>
*''E. coli'' 70S ribosome intermediates in a key conformational change: [[3i1m]],  [[3i1n]], [[3i1o]], [[3i1p]], [[3i1q]], [[3i1r]],[[3i1s]],[[3i1t]],[[3i1z]], [[3i20]], [[3i21]], and [[3i22]].<br>
*''E. coli'' ribosome in complex with the atypical aminoglycoside antibiotic hygromycin B: [[3df1]], [[3df2]],[[3df3]], and [[3df4]].<br>
*Structural basis of a mechanism of hydrolytic release of the newly formed polypeptide by the large subunit that may be analogous to that used by release factors:[[3cma]] and [[3cme]]
*Elongation factor P bound to the 70S ribosome: [[3huw]], [[3hux]], [[3huy]], and [[3huz]].<br>
*''Thermus thermophilus'' 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase): [2xfz],[2xg0],[2xg1], and [2xg2]</br>
*70S ribosome in complex with Ef-Tu and and aminoacyl-tRNA (P- and E- site tRNAs are also present): [[2wrn]], [[2wro]], [[2wrq]], and [[2wrr]]<br>
*70S ribosome in complex with EF-G (P- and E- site tRNAs are also present): [[2wri]] , [[2wrj]], [[2wrk]], and [[2wrl]]<br>
*Structure of stalled ribosome rescuing factor, Yaej, bound to the ''Thermus thermophilus'' 70S Ribosome: [[4dh9]], [[4dha]], [[4dhb]], and [[4dhc]]<br>
* EF-G–Ribosome Complexes (''Thermus thermophilus'') Trapped in Intermediate States of Translocation with β,γ-imidoguanosine 5′-triphosphate (GDPNP) or fusidic acid: [[4kcy|4kcy with GDPNP-I]], [[4kcz|4kcz with GDPNP-I]], [[4kd0|4kd0 with GDPNP-I]], [[4kd2|4kd2 with GDPNP-I]], [[4kbt|4kbt with GDPNP-2]], [[4kbu|4kbu with GDPNP-2]], [[4kbv|4kbv with GDPNP-2]], [[4kbw|4kbw with GDPNP-2]], [[4kd8|4kd8 with Fus-3.6]], [[4kd9|4kd9 with Fus-3.6]], [[4kda|4kda with Fus-3.6]], [[4kdb|4kdb with Fus-3.6]], [[4kdg|4kdg with Fus-4.2]], [[4kdh|4kdh with Fus-4.2]], [[4kdj|4kdj with Fus-4.2]], [[4kdk|4kdk with Fus-4.2]]<br>
*Elongation Factor G Bound to the ''Thermus thermophilus'' Ribosome in an Intermediate State of Translocation :[[4juw]] and [[4jux]]<br>
*Control of Ribosomal Subunit Rotation by Elongation Factor G (''Escherichia coli''): [[4kix]], [[4kiy]], [[4kiz]], [[4kj0]], [[4kj1]], [[4kj2]], [[4kj3]], [[4kj4]], [[4kj5]], [[4kj6]], [[4kj7]], [[4kj8]], [[4kj9]], [[4kja]], [[4kjb]], and [[4kjc]]<br>
*[[3o2z]], [[3o30]], [[3o58]], and [[3o5h]] are the subunits of the eukaryotic 80S ribosome of the baker's yeast ''Saccharomyces cerevisiae''.<br>
*The eukaryotic (''S. cerevisiae'') ribosome at atomic resolution using cryo-EM reconstruction and protein [[Theoretical models#Homology Models|homology modeling]]: [[3jyx]], [[3jyw]], and [[3jyv]] <br>
*The bacterial ''B. subtilis'' 50S ribosome assembly intermediates at atomic resolution using cryo-EM reconstruction:[[3j3v]] and [[3j3w]]
*''Drosophila melanogaster'' 80S ribosome in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps: [[3j38]], [[3j39]], [[3j3c]], [[3j3e]]
*Human 80S ribosome in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps: [[3j3a]], [[3j3b]], [[3j3d]], [[3j3f]]
*High-resolution cryo-electron microscopy structure of the ''Trypanosoma brucei'' ribosome: [[3zeq]], [[3zex]],[[3zey]], [[3zf7]]
*High-resolution cryo-electron microscopy structure of the large subunit of the mammalian mitochondrial ribosome: [[4ce4]]


==See Also==
==See Also==
* [[Nobel Prizes for 3D Molecular Structure]]
* [[Nobel Prizes for 3D Molecular Structure]]
* [[Highest impact structures]] of all time
* [[Highest impact structures]] of all time
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* [[DNA Replication, Transcription and Translation]]
* [[DNA Replication, Transcription and Translation]]
* [[tRNA]]
* [[tRNA]]
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]]
* [[LepA|Escherichia coli LepA, the ribosomal back translocase]]
* [[LepA|Escherichia coli LepA, the ribosomal back translocase]]
* [[Extremophiles]]
* [[Extremophiles]]
*[[RNA]]
* [[RNA]]
* [[Ribozyme]]
* [[Ribozyme]]
* For Spanish see [[Ribosoma 70S]]


==References==
==References==
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[[Category:Topic Page]]
[[Category:Topic Page]]
[[Category:Translation]]
[[Category:Translation]]
[[Category:Ribosome]]
[[Category: BioMolViz]]
[[Category: Macromolecular Assemblies]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Eric Martz, Eran Hodis, Jaime Prilusky, David Canner, Alexander Berchansky, Michal Harel, Joel L. Sussman, Margaret Franzen
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