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[[Image:Screen capture of 70S white background spacefill tRNAS.jpg|left|300px]]<br />
[[Image:Screen capture of 70S white background spacefill tRNAS.jpg|left|300px]]<br />


 
__NOTOC__


'''The Ribosome'''<br>
'''The Ribosome'''<br>

Revision as of 12:30, 25 May 2014





The Ribosome
The protein synthesis machine of cells
shown with the 3 transfer RNAs and messenger RNA bound.



IntroductionIntroduction

 
Drag the structure with the mouse to rotate
The Ribosome (1jgo and 1giy), resolution 5.5Å ().

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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 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.

Nobel Prize Winners and Other ContributorsNobel Prize Winners and Other Contributors

Venkatraman Ramakrishnan of the M.R.C. Laboratory of Molecular Biology in Cambridge, England; Thomas A. Steitz of Yale University; and Ada E. Yonath of the Weizmann Institute of Science in Rehovot, Israel have been awarded the the 2009 Nobel Prize in Chemistry[1] for their landmark work revealing the atomic details of the molecular machine that make proteins in all cells, the ribosome. Their findings are the gloriously enlightening culmination of years of work[2], first heralded by Ada Yonath's report of crystals in 1980[3]. Others made significant contributions to the detailed structure of this machine, as poignantly summarized by Jeremy Berg, current Director of National Institute of General Medical Sciences, in his announcement

The Nobel committee has the daunting challenge of limiting itself to up to three laureates for each prize. Several other long-time NIGMS grantees who also contributed greatly to our understanding of the structure and function of the ribosome include Peter Moore, Harry Noller and Joachim Frank.

The American Society for Biochemistry and Molecular Biology posted an announcement of the prize echoing this sentiment as well.

Impact of Ribosome StructureImpact of Ribosome Structure

The ribosome ranks among the known structures with highest impact. Imagine the wonder and thrill at suddenly knowing how tens of proteins and large and small RNAs fit together into the elegant machines that serve as the protein factories in every cell and organelle of every organism on the planet. The immense size of the ribosome and each of the two individual ribosomal subunits that come together to form the complete ribosome that is active in translation made for a daunting task in structure determination. These structures were at the time they were first determined, and remain (in 2009), the largest asymmetric molecules solved crystallographically. In addition to providing us immense insight into the general molecular and atomic details of protein synthesis in every organism on earth, the development of new antibiotics are likely to rely on this ground-breaking work.

Ribosome ComponentsRibosome Components

The small subunit of the prokaryotic ribosome sediments at 30S[4]. 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. See also Large Ribosomal Subunit of Haloarcula.

Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain.

Thus, a complete functioning prokaryotic ribosome contains 7 RNA chains (including three tRNA's and one mRNA), 47 ribosomal protein chains, and one nascent protein chain. The total molecular mass is several million daltons.

The cytoplasmic ribosomes of eukaryotes are larger with more RNA and proteins. Eukaryotic cytoplasmic ribosomes also have an additional RNA in the large subunit, the 5.8S rRNA, that is about 150 nts and related to the 5' end of prokaryotic rRNA. In regards to the size, the ribosomal subunits of budding yeast and humans sediment at 40S and 60S; the complete ribosome sediments at 80S and it is generally about another million daltons larger than the prokaryotic one.

The Peptidyl Transferase Is A RibozymeThe Peptidyl Transferase Is A Ribozyme

The small subunit of the ribosome is the main site of decoding, directing the interaction of the messenger RNA codon with the anticodon stem-loops of the proper transfer RNA. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked. However, it is important to keep in mind that in the active ribosome the two subunits are in contact via bridges, and the actions in one subunit affect the other as the process of translation advances through the stages of initiation, elongation, and termination.

The initial determination of the atomic resolution structures of the subunits surprisingly revealed that RNA, but not protein, contributes directly to forming the site of both decoding and catalysis of peptide bond synthesis, with the ribosomal proteins only acting in an ancillary role, see ribozyme. (Examine the structural data concerning peptide bond synthesis here.) During the elongation stage of translation, new peptides are added to the carboxy-terminus of the growing nascent chain that is linked to the acceptor-end of the tRNA in the peptidyl or P site. As the nascent chain grows, it advances into a tunnel that passes through the large subunit, called the polypeptide exit tunnel. Several factors can interact at the site of extrusion of the nascent polypeptide chain to ensure proper folding or transport across a membrane. Additionally, during protein synthesis, many additional factors such as elongation factors (EF-Tu and EF-G) interact with the ribosome to elicit decoding and peptide bond synthesis accurately and efficiently. Structures of several of these factors in complex with the ribosome, as well as intermediate states in the process, are being observed now, building upon the first atomic structures.

First Atomic-Resolution Ribosome StructuresFirst Atomic-Resolution Ribosome Structures

The particular structures for which the Nobel prize was awarded were published in 2000 and were subsequently refined or improved upon. All these structures were determined using proteins from extremophiles. Here are the links to the Proteopedia entries:

  • Yonath lab original atomic-resolution structures[5][6]: Thermus thermophilus small ribosomal subunit - 1fka, improved in 1i94, 1i95, 1i96, and 1i97. Thermus thermophilus is a thermophilic eubacteria. Deinococcus radiodurans large ribosomal subunit - 1nkw, later refined to give 2zjr. Deinococcus radiodurans is a mesophilic eubacteria.
  • Ramakrishnan lab original atomic-resolution structures[7][8]: Thermus thermophilus 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.

The Thermus thermophilus 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).

  • Steitz and Moore labs original atomic-resolution structures[9][10]: Haloarcula marismortui large ribosomal subunit - 1ffk and later refined to give 1jj2, and then refined to give 1s72, and later 3cc2[11]. Related: 1ffz, 1fg0. Haloracula is a halophilic archaea. Assembled with the ribosomal RNAs (2,922 and 122 nucleotides long) in the structure 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).[12]

Proteopedia Topic Pages Covering the Ribosome and SubunitsProteopedia Topic Pages Covering the Ribosome and Subunits


3D structures of BAG family proteins3D structures of BAG family proteins

Updated on 25-May-2014

30S subunit + RNA30S subunit + RNA

2zm6, 1n36, 1j5e, 3oto - Tt30S ribosomal subunit+THX+16S RRNA – Thermus thermophiles
2vqe, 2vqf, 2uuc, 2e5l, 2uu9, 2uua, 2uub, 3pyn, 3pyq, 3pys, 3pyu - Tt30S ribosomal subunit+16S RRNA+RNA fragment
3kc4 - Ec30S ribosomal subunit - Escherichia coli
3i1m, 3i1o, 3df1, 3df3, 2vho, 2vhp, 2avy, 2aw7, 1pnx - Ec30S ribosomal subunit+16S RRNA
1i94, 1fka, 3uxs, 3uxt, 4dr1 - Tt30S ribosomal subunit+16S RRNA
4duy, 4duz, 4dv0, 4dv1, 4dv2, 4dv3, 4dv4, 4dv5, 4dv6, 4dv7 - Tt30S ribosomal subunit+16S RRNA (mutant)
4dr4, 4b3m, 4b3r, 4b3s, 4b3t - Tt30S ribosomal subunit+16S RRNA + mRNA
1p87 - Ec30S ribosomal subunit+16S RRNA – Cryo-EM
3bbn - s30S ribosomal subunit+16S RRNA – Cryo-EM – spinach

30S subunit + chain release factor30S subunit + chain release factor

3mr8, 3ms0 – Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+mRNA+16S RRNA
3d5a 3d5c - Tt30S ribosomal subunit+THX+chain release factor 1+P-site tRNA+E-site tRNA+mRNA +16S RRNA
3zvo - Tt30S ribosomal subunit+THX+P-site tRNA Met +mRNA +16S RRNA+chain release factor 3
2b64 - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA+chain release factor 1
2b9m - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA+chain release factor 2
2x9r, 2x9t, 2wh1, 2wh3 - Tt30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+mRNA +16S RRNA
3f1e, 3f1g - Tt30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+E-site tRNA +16S RRNA
4kfh, 4kfk - Tt30S ribosomal subunit+16S RRNA+ RF-2 + mRNA+ P-site tRNA fMet

30S subunit +tRNA+mRNA30S subunit +tRNA+mRNA

2hgi - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA fMet
4l6k, 4l6m - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA
2hgp - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+mRNA
3t1h, 3t1y - Tt30S ribosomal subunit+16S RRNA+tRNA Lys +mRNA
3tvf, 3tvg, 3uyd, 3uyf - Tt30S ribosomal subunit+16S RRNA+tRNA Leu + tRNA fMet + mRNA
3zn7, 3znd - Tt30S ribosomal subunit+16S RRNA+A-site tRNA Ile agmatidine + E-site tRNA Ile agmatidine + mRNA
3uz6, 3uz7, 3uzg, 3uzi - Tt30S ribosomal subunit+16S RRNA+tRNA Tyr + tRNA fMet + mRNA
2i2p, 2i2u - Ec30S ribosomal subunit+16S RRNA+tRNA Phe+mRNA
2hgr, 3v6u, 3v6v, 4ej9, 4eja - Tt30S ribosomal subunit+16S RRNA+tRNA Phe+tRNA fMet+mRNA
1yl4 – Tt30S ribosomal subunit+ tRNA Phe+16S RRNA+THRS mRNA operator
1pns - Ec30S ribosomal subunit+ tRNA Phe+16S RRNA+mRNA
3j13 - Ec30S ribosomal subunit+ P-site tRNA +16S RRNA+mRNA – Cryo-EM
3j0u, 3j0v, 3j0x, 3j0z, 3j10, 3j20 - Ec30S ribosomal subunit+ A-site tRNA + P-site tRNA +16S RRNA+mRNA – Cryo-EM
1xnq, 1xnr - Tt30S ribosomal subunit+THX+mRNA+tRNA anticodon+16S RRNA
4gkj, 4gkk - Tt30S ribosomal subunit +16S RRNA +THX + mRNA + tRNA Met
4jv5, 4jya, 4k0k, 4k0l - Tt30S ribosomal subunit +16S RRNA +THX + mRNA + ASL-tRNA

30S subunit +A-site tRNA30S subunit +A-site tRNA

2uxd, 2uxc - Tt30S ribosomal subunit+THX+A-site mRNA CGGG+tRNA anticodon+16S RRNA
1n32, 1n33 - Tt30S ribosomal subunit+THX+A-site mRNA fragment+tRNA anticodon+16S RRNA
1n34 - Tt30S ribosomal subunit+THX+A-site mRNA fragment +16S RRNA
1xmo, 1xmq - Tt30S ribosomal subunit+THX+A-site mRNA+tRNA anticodon+16S RRNA
2uxb - Tt30S ribosomal subunit+THX+A-site mRNA GGGU+tRNA anticodon+16S RRNA

30S subunit+P-site tRNA30S subunit+P-site tRNA

3i8g - Tt30S ribosomal subunit+P-site tRNA+mRNA +16S RRNA
3i8h, 3i9b, 3i9d - Tt30S ribosomal subunit+THX+P-site tRNA+mRNA +16S RRNA
1ibk - Tt30S ribosomal subunit+THX+P-site mRNA fragment +16S RRNA
2wwl - Ec30S ribosomal subunit+Poly-Ala chain+P-site tRNA+mRNA +16S RRNA
3i1q - Ec30S ribosomal subunit+P-site tRNA hairpin+mRNA
3i1s, 3i1z, 3i21 - Ec30S ribosomal subunit+P-site tRNA hairpin+mRNA +16S RNA
2om7 – TtRPS2+TtRPS12+TtRPL1+ P-site tRNA+16S RRNA fragment+23S RRNA fragment

30S subunit+A-site tRNA+P-site tRNA30S subunit+A-site tRNA+P-site tRNA

1ibl, 1ibm - Tt30S ribosomal subunit+THX+A-site mRNA fragment+P-site mRNA fragment+tRNA anticodon+16S RRNA

30S subunit+P-site tRNA+E-site tRNA30S subunit+P-site tRNA+E-site tRNA

2ow8 - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA+mRNA +16S RRNA
2b9o - Tt30S ribosomal subunit+THX+P-site tRNA Phe+E-site tRNA Phe+mRNA +16S RRNA
2qnh - Tt30S ribosomal subunit+THX+P-site tRNA+E-site tRNA+mRNA +16S RRNA
2wdg, 2wdh, 2wdk, 2wdm - Tt30S ribosomal subunit+THX+P-site tRNA+E-site tRNA+mRNA +16S RRNA+tRNA Phe

30S subunit+A-site tRNA+P-site tRNA+E-site tRNA30S subunit+A-site tRNA+P-site tRNA+E-site tRNA

2gy9, 2gyb - Ec30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA – Cryo-EM
1jgo, 1jgp, 1jgq, 1gix - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+tRNA Phe+mRNA +16S RRNA
4k0p - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA +mRNA +16S RRNA
3e1a, 3e1c - Ec30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA

30S subunit + antibiotics30S subunit + antibiotics

1i95, 1i97, 2hhh, 2f4v, 3oge, 3ogy, 3ohc, 3ohd, 3ohy, 3oi0, 3oi2, 3oi4, 4dr3 - Tt30S ribosomal subunit+16S RRNA+antibiotic
1hnx, 1hnw, 1hnz, 1fjg, 4aqy, 4dr5, 4dr6, 4dr7, 4khp - Tt30S ribosomal subunit+16S RRNA+mRNA fragment+antibiotic
2qbb, 2qb9, 1vs5, 1vs7 , 2qan, 2qal, 2qou, 2qow, 2qoy, 2qp0, 2z4k, 2z4m, 3oaq, 3oar, 3ofa, 3ofb, 3ofo, 3ofp, 3ofx, 3ofy, 3or9, 3ora - Ec30S ribosomal subunit+16S RRNA+antibiotic
4gaq, 4gas - Ec30S ribosomal subunit+16S RRNA+ mRNA + antibiotic
3sfs - Ec30S ribosomal subunit+16S RRNA+ mRNA + RF-3 + antibiotic
2j00, 2j02 - Tt30S ribosomal subunit+16S RRNA+paromomycin+P-site tRNA fMet+E-site tRNA Phe+mRNA
3knl, 3knm, 3knn, 3kno, 3knj, 3knh - Tt30S ribosomal subunit+P-site tRNA+A-site tRNA+E-site tRNA+mRNA +16S RRNA+ antibiotic
3uz3, 3uz4 - Tt30S ribosomal subunit+16S RRNA+tRNA Leu + tRNA fMet + mRNA + paromomycin
4g5k, 4g5m, 4g5t, 4g5v - Tt30S ribosomal subunit+16S RRNA + tRNA fMet + mRNA + antibiotics
3uzl, 3uzm - Tt30S ribosomal subunit+16S RRNA+tRNA Tyr + tRNA fMet + mRNA + paromomycin

30S subunit + ribosome recycling factor30S subunit + ribosome recycling factor

2qbd, 2qbf - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor
3r8n, 3r8o, 4gd1, 4gd2 - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor + mRNA + tRNA
2qbh, 2qbj - Ec30S ribosomal subunit+16S RRNA+ribosome recycling factor+gentamicin
2v46, 2v48 - Tt30S ribosomal subunit+16S RRNA+ribosome recycling factor+P-site tRNA Phe+mRNA+tRNA fMet

30S subunit + elongation factor30S subunit + elongation factor

2wri, 2wrk - Tt30S ribosomal subunit+THX+P-site tRNA+mRNA +16S RRNA+elongation factor G
2wrn, 2wrq - Tt30S ribosomal subunit+THX+A-site tRNA+mRNA +16S RRNA+elongation factor TU-4
3fic - Tt30S ribosomal subunit+THX+A-site tRNA+P-site tRNA+E-site tRNA+mRNA codon+16S RRNA+elongation factor TU-A
4abr - Tt30S ribosomal subunit+THX + E/P-site tRNA fMet +mRNA codon+16S RRNA+elongation factor TU
2y0u, 2y0w, 2y0y, 2y12, 2y10, 2y18, 2y14, 2y16 - Tt30S ribosomal subunit+THX+A-site tRNA+E-site tRNA+mRNA codon+16S RRNA+elongation factor TU
3fih - Ec30S ribosomal subunit+A-site tRNA Phe+P-site tRNA+mRNA +16S RRNA+elongation factor TU
3izv - Ec30S ribosomal subunit+A/T-site tRNA Phe +16S RRNA+elongation factor TU
3j18 - Ec30S ribosomal subunit+A/T-site tRNA Phe +16S RRNA+ mRNA + SSRA-binding protein + formyl-Met specific initiator tRNA + elongation factor G – Cryo-EM
3izw - Ec30S ribosomal subunit+A-site tRNA Phe +mRNA +16S RRNA+elongation factor TU
3huw, 3huy - Tt30S ribosomal subunit+THX+tRNA-Met+mRNA +16S RRNA+elongation factor P
4b8f, 4b8h - Tt30S ribosomal subunit+THX+RNA+mRNA +16S RRNA+elongation factor G
4btc, 4kdg, 4kdj - Tt30S ribosomal subunit+THX+RNA +16S RRNA+elongation factor G
4juw - Tt30S ribosomal subunit+THX+ tRNA Phe +16S RRNA + mRNA +elongation factor G
4kbt, 4kbv, 4kcy, 4kd0, 4kd8, 4kda - Tt30S ribosomal subunit+THX+ tRNA Met +16S RRNA + mRNA + viomycin + elongation factor G
4kiy, 4kj0, 4kj2, 4kj4, 4kj6, 4kj8, 4kja, 4kjc - Ec30S ribosomal subunit +16S RRNA + viomycin + elongation factor G

30S subunit + translation initiation factor30S subunit + translation initiation factor

1hr0 - Tt30S ribosomal subunit+THX+IF+16S RRNA
1i96 - Tt30S ribosomal subunit+THX+IF3+16S RRNA

30S subunit + various proteins30S subunit + various proteins

3kiq, 3kis, 3kiu, 3kix - Tt30S ribosomal subunit+toxin RelE+16S RRNA
2xfz, 2xg1 - Tt30S ribosomal subunit+colicin-E3 fragment+16S RRNA+mRNA+E-site tRNA+THX
1voq, 1vos , 1vov, 1vox, 1voz - Ec30S ribosomal subunit+protein Y+16S RRNA
3j36 - Ec30S ribosomal subunit+ tetracycline resistance protein +16S RRNA + mRNA + P-tRNA – Cryo-EM
1x18 – TtRPS2+TtRPS7+TtRPS11+TtRPS18+GTP-binding protein ERA+RNA fragments
4dh9, 4dhb - Tt30S ribosomal subunit +16S RRNA+mRNA+P-site tRNA fMet +THX + YAEJ
3v22, 3v24, 3v26, 3v28 - Tt30S ribosomal subunit +16S RRNA +THX + modulation factor
3v2c, 3v2e - Tt30S ribosomal subunit +16S RRNA +THX + ribosome-associated inhibitor
3j00 – EcRPS2 + 16S RRNA + FTSQ + apolipoprotein A-I
2ykr - EcRPS2 + 16S RRNA + GMPPNP + GTPase RSGA
4a2i - EcRPS2 + 16S RRNA + GTPase RSGA – Cryo EM
3uoq - EcRPS2 + 16S RRNA + mRNA + peptide chain release factor
4adv - EcRPS2 + 16S RRNA + methyltransferase – Cryo EM

40S ribosomal subunit40S ribosomal subunit

3jyv - Tl40S ribosomal subunit+RACK1+S19E+P-site tRNA – Thermomyces lanuginosus
2xzm, 2xzn - Tet40S ribosomal subunit+RACK1 – Tetrahymena thermophila
1s1h - y40S ribosomal subunit+18S RRNA+elongation factor 2 – Cryo-EM – yeast
3izb - y40S ribosomal subunit+ RACK1 – Cryo-EM
3o2z, 3o30 - y40S ribosomal subunit+ RACK1
3u5c, 3u5g - y40S ribosomal subunit+ RACK1 + suppressor protein SMT1
3iz6 - w40S ribosomal subunit+RACK1 – wheat
3j38 - Dm40S ribosomal subunit + EF-2 + guanine nucleotide-binding protein – Drosophila melanogaster – Cryo-EM
3j3a - h40S ribosomal subunit + EF-2 + guanine nucleotide-binding protein – human – Cryo-EM
4kzx - r40S ribosomal subunit+ RACK1 + EIF1 – rabbit – Cryo-EM
4kzy - r40S ribosomal subunit+ RACK1 + EIF1 + EIF1A – Cryo-EM
4kzz - r40S ribosomal subunit+ RACK1 + EIF1A + initiator tRNA – Cryo-EM
2zkq – d40S ribosomal subunit+RACK1+RRNA fragment – dog - Cryo-EM
3zey - Tb40S ribosomal subunit – Trypanosoma brucei – Cryo-EM
4bpe, 4bpn, 4bpo, 4bpp - r40S ribosomal subunit+ 18SRRNA + EIF1 + EIF1A

50S subunit+RNA50S subunit+RNA

2x9s, 2x9u, 3kni, 3knk, 3knm, 3kno, 3hux, 3huz, 2wdi, 2wdj 2wdl 1vsp, 2v47 , 2v49, 1vsa, 3pyo, 3pyr, 3pyt, 3pyv, 3v6w, 3v6x, 3zne, 4btd, 4ejb, 4ejc, 4k0m, 4k0q, 2wrj, 2wrl, 2wro, 2wrr, 2wh2, 2wh4, 2hgj, 2hgq, 2hgu,2j01, 2j03, 1yl3, 3i8i, 3f1f, 3f1h, 2b66, 2b9n, 2b9p, 1giy, 2xqe, 2y0v, 2y0x, 2y0z, 2y11, 2y13, 2y15, 2y17, 2y19, 3zvp, 4abs, 4b8g, 4b8i, 4jux, 4kbu, 4kbw, 4kcz, 4kd2, 4kd9, 4kdb, 4kdh, 4kdk, 4kfi, 4kfl - Tt50S subunit+5S RRNA+23S RRNA
2xg0, 2xg2, 3kir, 3kit, 3kiw, 3kiy – Tt50S subunit+RNA fragments
3fin, 2xtg, 2xux - Tt50S subunit+5S RRNA+23S RRNA – Cryo-EM
2wwq – Ec 50S subunit+5S RRNA+23S RRNA+mRNA+P-site tRNA
3i1n, 3i1p, 3i1r, 3i1t, 3i20, 3i22, 3e1b, 3e1d, 3df2, 3df4, 2vhn, 2qov, 2qox, 2i2t, 2i2v, 1vs6, 1vs8, 2aw4, 2awb, 3ofd, 3og0, 3oas, 3oat, 3uos, 3r8s, 3r8t, 3j37, 4kix, 4kiz, 4kj1, 4kj3, 4kj5, 4kj7, 4kj9, 4kjb - Ec50S subunit+5S RRNA+23S RRNA
3fik, 2gya, 2gyc, 1p85, 1p86, 3izt, 3izu, 3j0t, 3j0w, 3j0y, 3j11, 3j12, 3j14, 3j19 - Ec50S subunit+5S RRNA+23S RRNA – Cryo-EM
3kcr - Ec50S subunit+5S RRNA+23S RRNA+preprotein translocase
3bbo - s50S subunit+5S RRNA+23S RRNA+4.8S RRNA – Cryo-EM
2zjq, 2zjr, 1nkw - Dr50S subunit+5S RRNA+23S RRNA – Deinococcus radiodurans
2qa4, 3cc2, 1s72, 4hub, 1kqs, 1qvg, 1jj2, 1ffk - Hm50S subunit+5S RRNA+23S RRNA – Haloarcula marismortui
3cc7, 3cce, 3ccj, 3ccl, 3ccm, 3ccq, 3ccr, 3ccs, 3ccu, 3ccv - Hm50S subunit+5S RRNA+23S RRNA (mutant)
1yj9 - Hm50S subunit (mutant)+5S RRNA+23S RRNA
1qvf- Hm50S subunit+5S RRNA+23S RRNA + deacylated tRNA minihelix
1q86 - Hm50S subunit+5S RRNA+23S RRNA+CCA-Phe-caproic acid-biotin
3cma, 3cme, 1vq8, 1vq9, 1m90 - Hm50S subunit+5S RRNA+23S RRNA+CCA+CCA-Phe-CAP-BIO
1vq4, 1vq5, 1vq7, 1vql, 1vqm, 1vqp – Hm50S subunit+5S RRNA+23S RRNA+transition state analog
1vq6, 1vqk, 1vqn – Hm50S subunit+5S RRNA+23S RRNA+ c-hpmn+CCA-Phe-caproic acid-biotin
1vqo – Hm50S subunit+5S RRNA+23S RRNA+ CCPMN
3iy9 – 50S subunit – Leishmania taretolae
2ftc – 50S subunit+5S RRNA+23S RRNA – bovine - Cryo_EM
3j21 – 50S subunit + P0 + LX – Pyrococcus furiosus – Cryo EM
3j3v, 3j3w - 50S subunit+5S RRNA+23S RRNA – Bacillus subtilis

50S subunit + antibiotics50S subunit + antibiotics

3dll, 2zjp, 3cf5, 1xbp, 1sm1, 1nwx, 1nwy, 3pio, 3pip - Dr50S subunit+5S RRNA+23S RRNA+general stress protein Ctc+ antibiotic
4io9, 4ioa, 4ioc - Dr50S subunit+5S RRNA+23S RRNA+ antibiotics
2qba, 2qbc, 4gar, 4gau, 2qam, 2qao, 2qoz, 2qp1, 3ofc, 3ofz, 3ofq, 3ofr, 1vt2, 3orb, 4l6j, 4l6l - Ec50S subunit+5S RRNA+23S RRNA+ antibiotics
3i55 3i56, 3g4s, 3g4e, 3g71, 2qex, 3cc4, 3cd6, 1yhq, 1yi2, 1yij, 1yjn, 1yjw, 2otj, 2otl, 1yit, 1k73, 1kc8, 1k8a, 1k9m, 1kd1, 1m1k, 3cpw, 1yit, 1q7y, 1q81, 1q82, 1n8r, 1nji, 3cxc - Hm50S subunit+5S RRNA+23S RRNA + antibiotics
3oh5, 3oh7, 3ohj, 3ohk, 3ohz, 3oi1, 3oi3, 3oi5 - Tt50S subunit+5S RRNA+23S RRNA+antibiotic

60S subunit60S subunit

3jyw - 60S subunit – Thermomyces lanuginosus – Cryo-EM
1s1i, 1s1h - y60S ribosomal subunit+ 5.8S RRNA+ 5S RRNA – Cryo-EM
3izs - y60S subunit – Cryo-EM
3u5e, 3u5i - y60S subunit
3o58, 3o5h - y60S ribosomal subunit+ 5.8S RRNA+ 5S RRNA + 25S RRNA
3izr, 3izt, 3izu, 3izs - w60S subunit
3j39 – Dm60S subunit – Cryo-EM
3j3b – h60S subunit – Cryo-EM
4a17, 4a1a, 4a1c, 4a1e - Tet60S ribosomal subunit + 5S RRNA + 5.8S RRNA
3zf7 - Tb60S subunit - Cryo EM

large + small ribosomal subunitlarge + small ribosomal subunit

1ml5 - Ec50S ribosomal subunit+30S ribosomal subunit+THX+chain release factor 2+P-site tRNA+tRNA Phe+mRNA fragment+23S RRNA+5S RRNA+16S RRNA – Cryo-EM
2zkr - d60S ribosomal subunit+30S ribosomal subunit+28S RRNA+5.8S RRNA – Cryo-EM
3j0l - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments – Cryo-EM
3j0o, 3j0p, 3j0q - r60S ribosomal subunit+40S ribosomal subunit+RRNA fragments+ mRNA fragments + tRNA – Cryo-EM

50S subunit + ribosome releasing factor (RRF)50S subunit + ribosome releasing factor (RRF)

2qbe, 2qbg, 2qbi, 2qbk, 2z4l, 2z4n - Ec50S subunit+5S RRNA+23S RRNA+RRF
2rdo - Ec50S subunit+5S RRNA+23S RRNA+EF-G+RRF – Cryo-EM
3j0d - Tt50S subunit+5S RRNA+23S RRNA+RRF – Cryo-EM

50S subunit + various proteins50S subunit + various proteins

2vhm - Ec50S subunit+5S RRNA+23S RRNA+PDF C-terminal helix
2j28 - Ec50S subunit+5S RRNA+23S RRNA+signal recognition particle – Cryo-EM
1vor, 1vou, 1vow, 1voy, 1vp0, 1pnu, 1pny - Ec50S subunit+5S RRNA+23S RRNA+general stress protein Ctc
3j01 - Ec 50S subunit+5S RRNA+23S RRNA + SECYE – Cryo-EM
1w2b - Hm50S subunit+5S RRNA+23S RRNA+trigger factor N-terminal

60S subunit + various proteins60S subunit + various proteins

4a18, 4a19, 4a1b, 4a1d - Tet60S subunit+ 26S RRNA+ translation initiation factor 6
3izs – y60S subunit + P0 + P1 + P2 - Cryo EM
3u5i – y60S subunit + P0
4b6a – y60S subunit + P0 + P1 + P2 + ARX1 - Cryo EM
3o5h – y60S subunit + 5S RRNA + 5.8S RRNA + 25S RRNA + P0
3j39 – Dm60S subunit + P0 – Drosophila melanogaster - Cryo EM
3j3b – h60S subunit + P0 + P1 + P2 – human - Cryo EM


See AlsoSee Also

ReferencesReferences

  1. ↑ Nobel Prizes for 3D Molecular Structure.
  2. ↑ Service RF. Chemistry Nobel. Honors to researchers who probed atomic structure of ribosomes. Science. 2009 Oct 16;326(5951):346-7. PMID:19833925 doi:326/5951/346
  3. ↑ Yonath A, Mussig J, Tesche B, Lorenz S, Erdmann VA, Wittmann HG. Crystallization of the large ribosomal subunits from Bacillus stearothermophilus. Biochem. Internat. 1980 1:428-435.
  4. ↑ Svedberg unit in Wikipedia
  5. ↑ Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 2000 Sep 1;102(5):615-23. PMID:11007480
  6. ↑ Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001 Nov 30;107(5):679-88. PMID:11733066
  7. ↑ Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39. PMID:11014182 doi:http://dx.doi.org/10.1038/35030006
  8. ↑ Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000 Sep 21;407(6802):340-8. PMID:11014183 doi:10.1038/35030019
  9. ↑ Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PMID:10937989
  10. ↑ Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000 Aug 11;289(5481):920-30. PMID:10937990
  11. ↑ Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA. Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. J Mol Biol. 2008 Jun 6;379(3):505-19. Epub 2008 Apr 8. PMID:18455733 doi:http://dx.doi.org/10.1016/j.jmb.2008.03.075
  12. ↑ Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PMID:10937989

Additional Literature and ResourcesAdditional Literature and Resources

[xtra 1][xtra 2][xtra 3][xtra 4][xtra 5][xtra 6][xtra 7][xtra 8][xtra 9][xtra 10]

  1. ↑ Moore PB. The ribosome returned. J Biol. 2009;8(1):8. Epub 2009 Jan 26. PMID:19222865 doi:10.1186/jbiol103
  2. ↑ Schmeing TM, Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature. 2009 Oct 29;461(7268):1234-42. Epub 2009 Oct 18. PMID:19838167 doi:10.1038/nature08403
  3. ↑ Ramakrishnan V, Moore PB. Atomic structures at last: the ribosome in 2000. Curr Opin Struct Biol. 2001 Apr;11(2):144-54. PMID:11297922
  4. ↑ Rodnina MV, Wintermeyer W. The ribosome goes Nobel. Trends Biochem Sci. 2010 Jan;35(1):1-5. Epub 2009 Dec 2. PMID:19962317 doi:10.1016/j.tibs.2009.11.003
  5. ↑ Sprinzl M, Erdmann VA. Protein biosynthesis on ribosomes in molecular resolution: Nobel Prize for chemistry 2009 goes to three chemical biologists. Chembiochem. 2009 Dec 14;10(18):2851-3. PMID:19938030 doi:10.1002/cbic.200900652
  6. ↑ Bashan A, Yonath A. Correlating ribosome function with high-resolution structures. Trends Microbiol. 2008 Jul;16(7):326-35. Epub 2008 Jun 9. PMID:18547810 doi:10.1016/j.tim.2008.05.001
  7. ↑ Korostelev A, Noller HF. The ribosome in focus: new structures bring new insights. Trends Biochem Sci. 2007 Sep;32(9):434-41. Epub 2007 Aug 30. PMID:17764954 doi:10.1016/j.tibs.2007.08.002
  8. ↑ Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008 Mar;9(3):242-53. PMID:18292779 doi:10.1038/nrm2352
  9. ↑ Zimmerman E, Yonath A. Biological implications of the ribosome's stunning stereochemistry. Chembiochem. 2009 Jan 5;10(1):63-72. PMID:19089882 doi:10.1002/cbic.200800554
  10. ↑ Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res. 2013 Jun 14. PMID:23771137 doi:10.1093/nar/gkt513

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