Difference between revisions of "Ribosome"
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| + | '''Most genes encoding ribosomal proteins are essential and many ribosomal proteins belong to the small set of [[universally conserved proteins]].''' | ||
| + | |||
| + | ==[http://www.proteopedia.org/wiki/index.php/Ribosome Structure of the ribosome]== | ||
| + | * [http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-6306 EMD-6306] ([[MifM]]-stalled [[ribosome]] complex) {{PubMed|25903689}} | ||
| + | * [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=3J9W 3J9W] ([[MifM]]-stalled [[ribosome]] complex) {{PubMed|25903689}} | ||
| + | * [http://https://www.rcsb.org/structure/8QCQ AdpA-stalled ribosomal complex] {{PubMed|38503735}} | ||
| + | |||
==Proteins of the large subunit== | ==Proteins of the large subunit== | ||
| − | * [[rpmGA| | + | * [[rplA|L1]] |
| + | * [[rplB|L2]] | ||
| + | * [[rplC|L3]] | ||
| + | * [[rplD|L4]] | ||
| + | * [[rplE|L5]] | ||
| + | * [[rplF|L6]] | ||
| + | * [[rplI|L9]] | ||
| + | * [[rplJ|L10]] | ||
| + | * [[rplK|L11]] | ||
| + | * [[rplL|L12]] | ||
| + | * [[rplM|L13]] | ||
| + | * [[rplN|L14]] | ||
| + | * [[rplO|L15]] | ||
| + | * [[rplP|L16]] | ||
| + | * [[rplQ|L17]] | ||
| + | * [[rplR|L18]] | ||
| + | * [[rplS|L19]] | ||
| + | * [[rplT|L20]] | ||
| + | * [[rplU|L21]] | ||
| + | * [[rplV|L22]] | ||
| + | * [[rplW|L23]] | ||
| + | * [[rplX|L24]] | ||
| + | * [[rpmA|L27]] | ||
| + | * [[rpmB|L28]] | ||
| + | * [[rpmC|L29]] | ||
| + | * [[rpmD|L30]] | ||
| + | * [[rpmE|L31]] | ||
| + | * [[rpmF|L32]] | ||
| + | * [[rpmGA|L33a]] | ||
| + | * [[rpmGB|L33b]] | ||
| + | * [[rpmH|L34]] | ||
| + | * [[rpmI|L35]] | ||
| + | * [[rpmJ|L36]] | ||
==Proteins of the small subunit== | ==Proteins of the small subunit== | ||
| + | * [[ypfD|S1]] | ||
| + | * [[rpsB|S2]] | ||
| + | * [[rpsC|S3]] | ||
| + | * [[rpsD|S4]] | ||
| + | * [[rpsE|S5]] | ||
| + | * [[rpsF|S6]] | ||
| + | * [[rpsG|S7]] | ||
| + | * [[rpsH|S8]] | ||
| + | * [[rpsI|S9]] | ||
| + | * [[rpsJ|S10]] | ||
| + | * [[rpsK|S11]] | ||
| + | * [[rpsL|S12]] | ||
| + | * [[rpsM|S13]] | ||
| + | * [[rpsN|S14]] | ||
| + | * [[rpsO|S15]] | ||
| + | * [[rpsP|S16]] | ||
| + | * [[rpsQ|S17]] | ||
| + | * [[rpsR|S18]] | ||
| + | * [[rpsS|S19]] | ||
| + | * [[rpsT|S20]] | ||
| + | * [[rpsU|S21]] | ||
==Proteins that are part of the ribosome only under specific conditions== | ==Proteins that are part of the ribosome only under specific conditions== | ||
* [[Ctc]]: present in the large subunit under stress conditions | * [[Ctc]]: present in the large subunit under stress conditions | ||
| − | |||
* [[RpmGC]]: replaces [[rpmGA|L33]] under conditions of zinc limitation | * [[RpmGC]]: replaces [[rpmGA|L33]] under conditions of zinc limitation | ||
| + | * [[YbxF]]: L7 family, associated to the ribosome during logarithmic growth | ||
| + | * [[YhzA]]: replaces [[rpmE|L31]] under conditions of zinc limitation | ||
| + | * [[YtiA]]: replaces [[rpsN|S14]] under conditions of zinc limitation | ||
| + | |||
| + | ==Proteins that are similar to ribosomal proteins== | ||
| + | * [[YfjL]] | ||
| + | * [[YlxQ]] | ||
| + | * [[YpfD]] | ||
| + | |||
| + | ==Related pages== | ||
| + | * [[5S rRNA]] | ||
| + | * [[16S rRNA]] | ||
| + | * [[23S rRNA]] | ||
| + | * [[translation]] | ||
| + | |||
| + | ==Back to [[Protein-protein interactions]]== | ||
| + | |||
| + | ==Important original publications== | ||
| + | <pubmed>22848659 23420519 23002217 23700310 24186064 25182490 25132179 25903689 24500425 25775265 25775268 25707802 ,27382067 27873260 | ||
| + | </pubmed> | ||
==Reviews on ribosome structure and function== | ==Reviews on ribosome structure and function== | ||
| − | <pubmed> 19838167 17574829 16962654 16959973 12370012 </pubmed> | + | <pubmed> 19838167 17574829 16962654 16959973 12370012 20393556 19653700 21529161 21548786 23433801 23700310 </pubmed> |
Latest revision as of 17:27, 20 March 2024
Most genes encoding ribosomal proteins are essential and many ribosomal proteins belong to the small set of universally conserved proteins.
Contents
- 1 Structure of the ribosome
- 2 Proteins of the large subunit
- 3 Proteins of the small subunit
- 4 Proteins that are part of the ribosome only under specific conditions
- 5 Proteins that are similar to ribosomal proteins
- 6 Related pages
- 7 Back to Protein-protein interactions
- 8 Important original publications
- 9 Reviews on ribosome structure and function
Structure of the ribosome
- EMD-6306 (MifM-stalled ribosome complex) PubMed
- 3J9W (MifM-stalled ribosome complex) PubMed
- AdpA-stalled ribosomal complex PubMed
Proteins of the large subunit
- L1
- L2
- L3
- L4
- L5
- L6
- L9
- L10
- L11
- L12
- L13
- L14
- L15
- L16
- L17
- L18
- L19
- L20
- L21
- L22
- L23
- L24
- L27
- L28
- L29
- L30
- L31
- L32
- L33a
- L33b
- L34
- L35
- L36
Proteins of the small subunit
Proteins that are part of the ribosome only under specific conditions
- Ctc: present in the large subunit under stress conditions
- RpmGC: replaces L33 under conditions of zinc limitation
- YbxF: L7 family, associated to the ribosome during logarithmic growth
- YhzA: replaces L31 under conditions of zinc limitation
- YtiA: replaces S14 under conditions of zinc limitation
Proteins that are similar to ribosomal proteins
Related pages
Back to Protein-protein interactions
Important original publications
Sina Schäkermann, Pascal Prochnow, Julia E Bandow
Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research.
Methods Mol Biol: 2017, 1520;291-306
[PubMed:27873260]
[WorldCat.org]
[DOI]
(I p)
Brett Thurlow, Joseph H Davis, Vivian Leong, Trevor F Moraes, James R Williamson, Joaquin Ortega
Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit.
Nucleic Acids Res: 2016, 44(20);9918-9932
[PubMed:27382067]
[WorldCat.org]
[DOI]
(I p)
Daniel Sohmen, Shinobu Chiba, Naomi Shimokawa-Chiba, C Axel Innis, Otto Berninghausen, Roland Beckmann, Koreaki Ito, Daniel N Wilson
Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Nat Commun: 2015, 6;6941
[PubMed:25903689]
[WorldCat.org]
[DOI]
(I e)
Yury S Polikanov, Sergey V Melnikov, Dieter Söll, Thomas A Steitz
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly.
Nat Struct Mol Biol: 2015, 22(4);342-344
[PubMed:25775268]
[WorldCat.org]
[DOI]
(I p)
Jonas Noeske, Michael R Wasserman, Daniel S Terry, Roger B Altman, Scott C Blanchard, Jamie H D Cate
High-resolution structure of the Escherichia coli ribosome.
Nat Struct Mol Biol: 2015, 22(4);336-41
[PubMed:25775265]
[WorldCat.org]
[DOI]
(I p)
Niels Fischer, Piotr Neumann, Andrey L Konevega, Lars V Bock, Ralf Ficner, Marina V Rodnina, Holger Stark
Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.
Nature: 2015, 520(7548);567-70
[PubMed:25707802]
[WorldCat.org]
[DOI]
(I p)
Genki Akanuma, Ako Kobayashi, Shota Suzuki, Fujio Kawamura, Yuh Shiwa, Satoru Watanabe, Hirofumi Yoshikawa, Ryo Hanai, Morio Ishizuka
Defect in the formation of 70S ribosomes caused by lack of ribosomal protein L34 can be suppressed by magnesium.
J Bacteriol: 2014, 196(22);3820-30
[PubMed:25182490]
[WorldCat.org]
[DOI]
(I p)
Yury S Polikanov, Thomas A Steitz, C Axel Innis
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
Nat Struct Mol Biol: 2014, 21(9);787-93
[PubMed:25132179]
[WorldCat.org]
[DOI]
(I p)
Kurt Fredrick, Michael Ibba
The ABCs of the ribosome.
Nat Struct Mol Biol: 2014, 21(2);115-6
[PubMed:24500425]
[WorldCat.org]
[DOI]
(I p)
Lars V Bock, Christian Blau, Gunnar F Schröder, Iakov I Davydov, Niels Fischer, Holger Stark, Marina V Rodnina, Andrea C Vaiana, Helmut Grubmüller
Energy barriers and driving forces in tRNA translocation through the ribosome.
Nat Struct Mol Biol: 2013, 20(12);1390-6
[PubMed:24186064]
[WorldCat.org]
[DOI]
(I p)
Ningning Li, Yuling Chen, Qiang Guo, Yixiao Zhang, Yi Yuan, Chengying Ma, Haiteng Deng, Jianlin Lei, Ning Gao
Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.
Nucleic Acids Res: 2013, 41(14);7073-83
[PubMed:23700310]
[WorldCat.org]
[DOI]
(I p)
Fabian M Commichau, Nico Pietack, Jörg Stülke
Essential genes in Bacillus subtilis: a re-evaluation after ten years.
Mol Biosyst: 2013, 9(6);1068-75
[PubMed:23420519]
[WorldCat.org]
[DOI]
(I p)
Genki Akanuma, Hideaki Nanamiya, Yousuke Natori, Koichi Yano, Shota Suzuki, Shuya Omata, Morio Ishizuka, Yasuhiko Sekine, Fujio Kawamura
Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation.
J Bacteriol: 2012, 194(22);6282-91
[PubMed:23002217]
[WorldCat.org]
[DOI]
(I p)
Alex Rosenberg, Lior Sinai, Yoav Smith, Sigal Ben-Yehuda
Dynamic expression of the translational machinery during Bacillus subtilis life cycle at a single cell level.
PLoS One: 2012, 7(7);e41921
[PubMed:22848659]
[WorldCat.org]
[DOI]
(I p)
Reviews on ribosome structure and function
Ningning Li, Yuling Chen, Qiang Guo, Yixiao Zhang, Yi Yuan, Chengying Ma, Haiteng Deng, Jianlin Lei, Ning Gao
Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.
Nucleic Acids Res: 2013, 41(14);7073-83
[PubMed:23700310]
[WorldCat.org]
[DOI]
(I p)
Katelyn McGary, Evgeny Nudler
RNA polymerase and the ribosome: the close relationship.
Curr Opin Microbiol: 2013, 16(2);112-7
[PubMed:23433801]
[WorldCat.org]
[DOI]
(I p)
Edward Ki Yun Leung, Nikolai Suslov, Nicole Tuttle, Raghuvir Sengupta, Joseph Anthony Piccirilli
The mechanism of peptidyl transfer catalysis by the ribosome.
Annu Rev Biochem: 2011, 80;527-55
[PubMed:21548786]
[WorldCat.org]
[DOI]
(I p)
Zahra Shajani, Michael T Sykes, James R Williamson
Assembly of bacterial ribosomes.
Annu Rev Biochem: 2011, 80;501-26
[PubMed:21529161]
[WorldCat.org]
[DOI]
(I p)
Sotaro Uemura, Colin Echeverría Aitken, Jonas Korlach, Benjamin A Flusberg, Stephen W Turner, Joseph D Puglisi
Real-time tRNA transit on single translating ribosomes at codon resolution.
Nature: 2010, 464(7291);1012-7
[PubMed:20393556]
[WorldCat.org]
[DOI]
(I p)
T Martin Schmeing, V Ramakrishnan
What recent ribosome structures have revealed about the mechanism of translation.
Nature: 2009, 461(7268);1234-42
[PubMed:19838167]
[WorldCat.org]
[DOI]
(I p)
Matthew A Lauber, William E Running, James P Reilly
B. subtilis ribosomal proteins: structural homology and post-translational modifications.
J Proteome Res: 2009, 8(9);4193-206
[PubMed:19653700]
[WorldCat.org]
[DOI]
(P p)
Veysel Berk, Jamie H D Cate
Insights into protein biosynthesis from structures of bacterial ribosomes.
Curr Opin Struct Biol: 2007, 17(3);302-9
[PubMed:17574829]
[WorldCat.org]
[DOI]
(P p)
Andrei Korostelev, Sergei Trakhanov, Martin Laurberg, Harry F Noller
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
Cell: 2006, 126(6);1065-77
[PubMed:16962654]
[WorldCat.org]
[DOI]
(P p)
Maria Selmer, Christine M Dunham, Frank V Murphy, Albert Weixlbaumer, Sabine Petry, Ann C Kelley, John R Weir, V Ramakrishnan
Structure of the 70S ribosome complexed with mRNA and tRNA.
Science: 2006, 313(5795);1935-42
[PubMed:16959973]
[WorldCat.org]
[DOI]
(I p)
Ada Yonath
High-resolution structures of large ribosomal subunits from mesophilic eubacteria and halophilic archaea at various functional States.
Curr Protein Pept Sci: 2002, 3(1);67-78
[PubMed:12370012]
[WorldCat.org]
[DOI]
(P p)
