Editing Ribosome (section)

== Structure ==
[[File:Peptide syn.svg|thumb|upright=1.3|Ribosomes assemble [[polymer]]ic protein molecules, the order of which is controlled by the [[messenger RNA]]'s molecule sequence.]]
[[File:Ribosome Structure.png|thumb|[[Ribosomal RNA]] composition for [[prokaryote]]s and [[eukaryote]]s]]

The ribosome is a complex cellular machine. It is largely made up of specialized RNA known as [[ribosomal RNA]] (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). The ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different sizes, known generally as the large and small subunits of the ribosome. Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. Because they are formed from two subunits of non-equal size, they are slightly longer on the axis than in diameter.

=== Prokaryotic ribosomes ===
Prokaryotic ribosomes are around 20&nbsp;[[Nanometre|nm]] (200&nbsp;[[Ångström|Å]]) in diameter and are composed of 65% rRNA and 35% [[ribosomal protein]]s.<ref>{{cite journal|author1-link=Charles Kurland| vauthors = Kurland CG |title=Molecular characterization of ribonucleic acid from Escherichia coli ribosomes|journal=Journal of Molecular Biology|volume=2|issue=2|pages=83–91|doi=10.1016/s0022-2836(60)80029-0|year=1960}}</ref> Eukaryotic ribosomes are between 25 and 30 [[Nanometre|nm]] (250–300 Å) in diameter with an rRNA-to-protein ratio that is close to 1.<ref>{{cite journal | vauthors = Wilson DN, Doudna Cate JH | title = The structure and function of the eukaryotic ribosome | journal = Cold Spring Harbor Perspectives in Biology | volume = 4 | issue = 5 | pages = a011536 | date = May 2012 | pmid = 22550233 | pmc = 3331703 | doi = 10.1101/cshperspect.a011536 }}</ref> [[Crystallography|Crystallographic]] work<ref>{{cite journal | vauthors = Nissen P, Hansen J, Ban N, Moore PB, Steitz TA | title = The structural basis of ribosome activity in peptide bond synthesis | journal = Science | volume = 289 | issue = 5481 | pages = 920–30 | date = August 2000 | pmid = 10937990 | doi = 10.1126/science.289.5481.920 | bibcode = 2000Sci...289..920N | s2cid = 8370119 | url = http://pdfs.semanticscholar.org/0baa/9ba2a4d098674984113142bbf1ffca35700c.pdf | archive-url = https://web.archive.org/web/20201130102727/http://pdfs.semanticscholar.org/0baa/9ba2a4d098674984113142bbf1ffca35700c.pdf | url-status = dead | archive-date = 2020-11-30 }}</ref> has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis. This suggests that the protein components of ribosomes do not directly participate in peptide bond formation catalysis, but rather that these proteins act as a scaffold that may enhance the ability of rRNA to synthesize protein (see: [[Ribozyme]]).

[[Image:010 small subunit-1FKA.gif|thumb|Molecular structure of the 30S subunit from ''[[Thermus thermophilus]]''.<ref name="Wimberly-2000"/> Proteins are shown in blue and the single RNA chain in brown.]]

The ribosomal subunits of [[prokaryote]]s and [[eukaryote]]s are quite similar.<ref name="Alberts-2002">{{cite book | vauthors = Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P | chapter = Membrane-bound Ribosomes Define the Rough ER | chapter-url = https://www.ncbi.nlm.nih.gov/books/NBK26841/#A2204 | title = Molecular Biology of the Cell | edition = 4th | location = New York | publisher = Garland Science | date = 2002 | isbn = 978-0-8153-4072-0 | pages = 342 }}</ref>

The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the [[Svedberg]] unit, a measure of the rate of [[sedimentation]] in [[centrifugation]] rather than size. This accounts for why fragment names do not add up: for example, bacterial 70S ribosomes are made of 50S and 30S subunits.

Prokaryotes have 70[[Svedberg|S]] ribosomes, each consisting of a small ([[30S]]) and a large ([[50S]]) subunit. ''E. coli'', for example, has a [[16S ribosomal RNA|16S]] RNA subunit (consisting of 1540 nucleotides) that is bound to 21 proteins. The large subunit is composed of a [[5S ribosomal RNA|5S]] RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 [[protein]]s.<ref name="Alberts-2002" />

:{| class="wikitable float-right" style="text-align:center"
|+ Ribosome of ''E. coli'' (a bacterium)<ref name="Garrett-2009" />{{rp|962}}
|-
! width="25%"| ribosome
! width="25%"| subunit
! width="25%"| rRNAs
! width="25%"| r-proteins
|-
| rowspan="3" | 70S || rowspan="2" | 50S || 23S (2904 [[Nucleotide|nt]]) || rowspan="2" | 31
|-
| 5S (120 nt)
|-
| 30S || 16S (1542 nt) || 21
|}

Affinity label for the tRNA binding sites on the ''E. coli'' ribosome allowed the identification of A and P site proteins most likely associated with the peptidyltransferase activity;<ref name="Tirumalai-2021a"/> labelled proteins are L27, L14, L15, L16, L2; at least L27 is located at the donor site, as shown by E. Collatz and A.P. Czernilofsky.<ref>{{cite journal | vauthors = Collatz E, Küchler E, Stöffler G, Czernilofsky AP | title = The site of reaction on ribosomal protein L27 with an affinity label derivative of tRNA Met f | journal = FEBS Letters | volume = 63 | issue = 2 | pages = 283–6 | date = April 1976 | pmid = 770196 | doi = 10.1016/0014-5793(76)80112-3 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Czernilofsky AP, Collatz EE, Stöffler G, Kuechler E | title = Proteins at the tRNA binding sites of Escherichia coli ribosomes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 71 | issue = 1 | pages = 230–4 | date = January 1974 | pmid = 4589893 | pmc = 387971 | doi = 10.1073/pnas.71.1.230 | bibcode = 1974PNAS...71..230C | doi-access = free }}</ref> Additional research has demonstrated that the S1 and S21 proteins, in association with the 3′-end of 16S ribosomal RNA, are involved in the initiation of translation.<ref>{{cite journal | vauthors = Czernilofsky AP, Kurland CG, Stöffler G | title = 30S ribosomal proteins associated with the 3'-terminus of 16S RNA | journal = FEBS Letters | volume = 58 | issue = 1 | pages = 281–4 | date = October 1975 | pmid = 1225593 | doi = 10.1016/0014-5793(75)80279-1 | doi-access = free }}</ref>

===Archaeal ribosomes===
Archaeal ribosomes share the same general dimensions of bacteria ones, being a 70S ribosome made up from a 50S large subunit, a 30S small subunit, and containing three rRNA chains. However, on the sequence level, they are much closer to eukaryotic ones than to bacterial ones. Every extra ribosomal protein archaea have compared to bacteria has a eukaryotic counterpart, while no such relation applies between archaea and bacteria.<ref>{{cite book | vauthors = Cullen KE |title=Encyclopedia of Life Science |date=2009 |publisher=Facts On File |location=New York |isbn=9780470015902 |chapter=Archaeal Ribosomes|pages=1–5 |doi=10.1002/9780470015902.a0000293.pub3|s2cid=243730576 }}</ref><ref name="Tirumalai-2021b">{{cite journal | vauthors = Tirumalai MR, Anane-Bediakoh D, Rajesh R, Fox GE | title = Net Charges of the Ribosomal Proteins of the ''S10'' and ''spc'' Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance | journal = Microbiol. Spectr. | volume = 9 | issue = 3 | pages = e0178221 | date = November 2021 | pmid = 34908470 | pmc = 8672879 | doi = 10.1128/spectrum.01782-21}}</ref><ref>{{cite journal | vauthors = Wang J, Dasgupta I, Fox GE | title = Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters | journal = Archaea | volume = 2 | issue = 4 | pages = 241–51 | date = 28 April 2009 | pmid = 19478915 | pmc =2686390 | doi = 10.1155/2009/971494 | doi-access = free }}</ref>

===Eukaryotic ribosomes===
{{main|Eukaryotic ribosome}}

Eukaryotes have 80S ribosomes located in their cytosol, each consisting of a [[Eukaryotic small ribosomal subunit (40S)|small (40S)]] and [[Eukaryotic large ribosomal subunit (60S)|large (60S) subunit]]. Their 40S subunit has an [[18S ribosomal RNA|18S RNA]] (1900 nucleotides) and 33 proteins.<ref name="Ben-Shem-2011">{{cite journal | vauthors = Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M | title = The structure of the eukaryotic ribosome at 3.0 Å resolution | journal = Science | volume = 334 | issue = 6062 | pages = 1524–9 | date = December 2011 | pmid = 22096102 | doi = 10.1126/science.1212642 | bibcode = 2011Sci...334.1524B | s2cid = 9099683 | doi-access = free }}</ref><ref name="Rabl-2011">{{cite journal | vauthors = Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N | title = Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1 | journal = Science | volume = 331 | issue = 6018 | pages = 730–6 | date = February 2011 | pmid = 21205638 | doi = 10.1126/science.1198308 | hdl = 20.500.11850/153130 | bibcode = 2011Sci...331..730R | s2cid = 24771575 | url = https://www.research-collection.ethz.ch/bitstream/20.500.11850/153130/1/eth-5105-01.pdf | hdl-access = free }}</ref> The large subunit is composed of a [[5S ribosomal RNA|5S RNA]] (120 nucleotides), [[28S ribosomal RNA|28S RNA]] (4700 nucleotides), a [[5.8S ribosomal RNA|5.8S RNA]] (160 nucleotides) subunits and 49 proteins.<ref name="Alberts-2002" /><ref name="Ben-Shem-2011"/><ref name="Klinge-2011">{{cite journal | vauthors = Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N | title = Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 | journal = Science | volume = 334 | issue = 6058 | pages = 941–8 | date = November 2011 | pmid = 22052974 | doi = 10.1126/science.1211204 | bibcode = 2011Sci...334..941K | s2cid = 206536444 }}</ref>

:{| class="wikitable float-right" style="text-align:center"
|+ eukaryotic cytosolic ribosomes (''R.&nbsp;norvegicus'')<ref name="Garrett-2009">{{cite book | vauthors = Garrett R, Grisham CM | title = Biochemistry | edition = 4th | publisher = Cengage Learning Services | date = 2009 | isbn = 978-0-495-11464-2 }}</ref>{{rp|65}}
|-
! width="25%"| ribosome
! width="25%"| subunit
! width="25%"| rRNAs
! width="25%"| r-proteins
|-
| rowspan="4" | 80S || rowspan="3" | 60S || 28S (4718 nt) || rowspan="3" | 49
|-
| 5.8S (160 nt)
|-
| 5S (120 nt)
|-
| 40S || 18S (1874 nt) || 33
|}

During 1977, Czernilofsky published research that used [[affinity label]]ing to identify tRNA-binding sites on rat liver ribosomes. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the [[peptidyl transferase]] center.<ref>{{cite journal | vauthors = Fabijanski S, Pellegrini M | title = Identification of proteins at the peptidyl-tRNA binding site of rat liver ribosomes | journal = Molecular & General Genetics | volume = 184 | issue = 3 | pages = 551–6 | year = 1977 | pmid = 6950200 | doi = 10.1007/BF00431588 | s2cid = 9751945 }}</ref>

=== Plastoribosomes and mitoribosomes ===
{{main|Mitochondrial ribosome|Chloroplast#Chloroplast ribosomes}}
In eukaryotes, ribosomes are present in [[mitochondria]] (sometimes called [[mitochondrial ribosome|mitoribosomes]]) and in [[plastid]]s such as [[chloroplast]]s (also called plastoribosomes). They also consist of large and small subunits bound together with [[protein]]s into one 70S particle.<ref name="Alberts-2002" /> These ribosomes are similar to those of bacteria and these organelles are thought to have originated as [[symbiotic bacteria]].<ref name="Alberts-2002" /> Of the two, chloroplastic ribosomes are closer to bacterial ones than mitochondrial ones are. Many pieces of ribosomal RNA in the mitochondria are shortened, and in the case of [[5S ribosomal RNA#Presence in organelle ribosomes|5S rRNA]], replaced by other structures in animals and fungi.<ref>{{cite journal | vauthors = Agrawal RK, Sharma MR | title = Structural aspects of mitochondrial translational apparatus | journal = Current Opinion in Structural Biology | volume = 22 | issue = 6 | pages = 797–803 | date = December 2012 | pmid = 22959417 | pmc = 3513651 | doi = 10.1016/j.sbi.2012.08.003 }}</ref> In particular, ''[[Leishmania]] tarentolae'' has a minimalized set of mitochondrial rRNA.<ref>{{cite journal | vauthors = Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK | title = Structure of a mitochondrial ribosome with minimal RNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 24 | pages = 9637–42 | date = June 2009 | pmid = 19497863 | pmc = 2700991 | doi = 10.1073/pnas.0901631106 | bibcode = 2009PNAS..106.9637S | doi-access = free }}</ref> In contrast, plant mitoribosomes have both extended rRNA and additional proteins as compared to bacteria, in particular, many pentatricopetide repeat proteins.<ref>{{cite journal | vauthors = Waltz F, Nguyen TT, Arrivé M, Bochler A, Chicher J, Hammann P, Kuhn L, Quadrado M, Mireau H, Hashem Y, Giegé P | title = Small is big in Arabidopsis mitochondrial ribosome | journal = Nature Plants | volume = 5 | pages = 106–117 | date = January 2019 | issue = 1 | doi = 10.1038/s41477-018-0339-y | pmid = 30626926 | s2cid = 58004990 }}</ref>

The [[cryptomonad]] and [[chlorarachniophyte]] algae may contain a [[nucleomorph]] that resembles a vestigial eukaryotic nucleus.<ref name="Archibald-2009">{{cite journal | vauthors = Archibald JM, Lane CE | title = Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction | journal = The Journal of Heredity | volume = 100 | issue = 5 | pages = 582–90 | year = 2009 | pmid = 19617523 | doi = 10.1093/jhered/esp055 | doi-access = free }}</ref> Eukaryotic 80S ribosomes may be present in the compartment containing the nucleomorph.<ref>{{Cite web|title=Specialized Internal Structures of Prokaryotes {{!}} Boundless Microbiology|url=https://courses.lumenlearning.com/boundless-microbiology/chapter/specialized-internal-structures-of-prokaryotes/|access-date=2021-09-24|website=courses.lumenlearning.com}}</ref>

===Making use of the differences===
The differences between the bacterial and eukaryotic ribosomes are exploited by [[medicinal chemistry|pharmaceutical chemists]] to create [[antibiotic]]s that can destroy a bacterial infection without harming the cells of the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not.<ref name="Recht-1999">{{cite journal | vauthors = Recht MI, Douthwaite S, Puglisi JD | title = Basis for prokaryotic specificity of action of aminoglycoside antibiotics | journal = The EMBO Journal | volume = 18 | issue = 11 | pages = 3133–8 | date = June 1999 | pmid = 10357824 | pmc = 1171394 | doi = 10.1093/emboj/18.11.3133 }}</ref> Even though [[mitochondria]] possess ribosomes similar to the bacterial ones, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the [[organelle]].<ref>{{cite journal | vauthors = O'Brien TW | title = The general occurrence of 55 S ribosomes in mammalian liver mitochondria | journal = The Journal of Biological Chemistry | volume = 246 | issue = 10 | pages = 3409–17 | date = May 1971 | doi = 10.1016/S0021-9258(18)62239-2 | pmid = 4930061 | doi-access = free }}</ref> A noteworthy counterexample is the antineoplastic antibiotic [[chloramphenicol]], which inhibits bacterial 50S and eukaryotic mitochondrial 50S ribosomes.<ref>{{Cite journal|date=1970-08-17|title=Chloramphenicol-lnduced Bone Marrow Suppression|url=https://jamanetwork.com/journals/jama/fullarticle/356164|journal=JAMA|language=en|volume=213|issue=7|pages=1183–1184|doi=10.1001/jama.1970.03170330063011|pmid=5468266|issn=0098-7484}}</ref> Ribosomes in chloroplasts, however, are different: Antibiotic resistance in chloroplast ribosomal proteins is a trait that has to be introduced as a marker, with genetic engineering.<ref>{{cite journal | vauthors = Newman SM, Boynton JE, Gillham NW, Randolph-Anderson BL, Johnson AM, Harris EH | title = Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events | journal = Genetics | volume = 126 | issue = 4 | pages = 875–88 | date = December 1990 | doi = 10.1093/genetics/126.4.875 | pmid = 1981764 | pmc = 1204285 }}</ref>

===Common properties===
The various ribosomes share a core structure, which is quite similar despite the large differences in size. Much of the RNA is highly organized into various [[RNA Tertiary Structure|tertiary structural motifs]], for example [[pseudoknot]]s that exhibit [[Nucleic acid tertiary structure#Coaxial stacking|coaxial stacking]]. The extra [[RNA]] in the larger ribosomes is in several long continuous insertions,<ref>{{cite journal | vauthors = Penev PI, Fakhretaha-Aval S, Patel VJ, Cannone JJ, Gutell RR, Petrov AS, Williams LD, Glass JB| title = Supersized ribosomal RNA expansion segments in Asgard archaea | journal = Genome Biology and Evolution | date = August 2020 | volume = 12 | issue = 10 | pages = 1694–1710 | pmid = 32785681 | doi = 10.1093/gbe/evaa170 | pmc = 7594248 | doi-access = free }}</ref> such that they form loops out of the core structure without disrupting or changing it.<ref name="Alberts-2002" /> All of the catalytic activity of the ribosome is carried out by the [[ribozyme|RNA]]; the proteins reside on the surface and seem to stabilize the structure.<ref name="Alberts-2002" />

===High-resolution structure===
[[Image:10 large subunit.gif|thumb|200px|right| '''Figure 4:''' Atomic structure of the 50S subunit from ''[[Haloarcula|Haloarcula marismortui]]''. Proteins are shown in blue and the two RNA chains in brown and yellow.<ref name="Ban-2000">{{cite journal | vauthors = Ban N, Nissen P, Hansen J, Moore PB, Steitz TA | title = The complete atomic structure of the large ribosomal subunit at 2.4 A resolution | journal = Science | volume = 289 | issue = 5481 | pages = 905–20 | date = August 2000 | pmid = 10937989 | doi = 10.1126/science.289.5481.905 | citeseerx = 10.1.1.58.2271 | bibcode = 2000Sci...289..905B }}</ref> The small patch of green in the center of the subunit is the active site.]]

The general molecular structure of the ribosome has been known since the early 1970s. In the early 2000s, the structure has been achieved at high resolutions, of the order of a few [[ångström]]s.

The first papers giving the structure of the ribosome at atomic resolution were published almost simultaneously in late 2000. The 50S (large prokaryotic) subunit was determined from the [[Archaea|archaeon]] ''Haloarcula marismortui''<ref name="Ban-2000"/> and the [[Bacteria|bacterium]] ''[[Deinococcus radiodurans]]'', and the structure of the 30S subunit was determined from the bacterium ''[[Thermus thermophilus]]''.<ref name="Wimberly-2000">{{cite journal | vauthors = Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V | title = Structure of the 30S ribosomal subunit | journal = Nature | volume = 407 | issue = 6802 | pages = 327–39 | date = September 2000 | pmid = 11014182 | doi = 10.1038/35030006 | bibcode = 2000Natur.407..327W | s2cid = 4419944 }}</ref><ref name="Schluenzen-2000">{{cite journal | vauthors = Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A | title = Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution | journal = Cell | volume = 102 | issue = 5 | pages = 615–23 | date = September 2000 | pmid = 11007480 | doi = 10.1016/S0092-8674(00)00084-2 | s2cid = 1024446 | doi-access = free }}</ref> These structural studies were awarded the Nobel Prize in Chemistry in 2009. In May 2001 these coordinates were used to reconstruct the entire ''[[Thermus thermophilus|T. thermophilus]]'' 70S particle at 5.5&nbsp;[[Ångström|Å]] resolution.<ref>{{cite journal | vauthors = Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH, Noller HF | title = Crystal structure of the ribosome at 5.5 A resolution | journal = Science | volume = 292 | issue = 5518 | pages = 883–96 | date = May 2001 | pmid = 11283358 | doi = 10.1126/science.1060089 | bibcode = 2001Sci...292..883Y | s2cid = 39505192 | doi-access = free }}</ref>

Two papers were published in November 2005 with structures of the ''[[Escherichia coli]]'' 70S ribosome. The structures of a vacant ribosome were determined at 3.5&nbsp;[[Ångström|Å]] resolution using [[X-ray crystallography]].<ref>{{cite journal | vauthors = Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH | title = Structures of the bacterial ribosome at 3.5 A resolution | journal = Science | volume = 310 | issue = 5749 | pages = 827–34 | date = November 2005 | pmid = 16272117 | doi = 10.1126/science.1117230 | bibcode = 2005Sci...310..827S | s2cid = 37382005 }}</ref> Then, two weeks later, a structure based on [[Cryogenic electron microscopy|cryo-electron microscopy]] was published,<ref>{{cite journal | vauthors = Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J | title = Structure of the E. coli protein-conducting channel bound to a translating ribosome | journal = Nature | volume = 438 | issue = 7066 | pages = 318–24 | date = November 2005 | pmid = 16292303 | pmc = 1351281 | doi = 10.1038/nature04133 | bibcode = 2005Natur.438..318M }}</ref> which depicts the ribosome at 11–15&nbsp;[[Ångström|Å]] resolution in the act of passing a newly synthesized protein strand into the protein-conducting channel.

The first atomic structures of the ribosome complexed with [[tRNA]] and [[mRNA]] molecules were solved by using X-ray crystallography by two groups independently, at 2.8&nbsp;[[Ångström|Å]]<ref>{{cite journal | vauthors = Selmer M, Dunham CM, Murphy FV, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V | title = Structure of the 70S ribosome complexed with mRNA and tRNA | journal = Science | volume = 313 | issue = 5795 | pages = 1935–42 | date = September 2006 | pmid = 16959973 | doi = 10.1126/science.1131127 | bibcode = 2006Sci...313.1935S | s2cid = 9737925 }}</ref> and at 3.7&nbsp;[[Ångström|Å]].<ref>{{cite journal | vauthors = Korostelev A, Trakhanov S, Laurberg M, Noller HF | title = Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements | journal = Cell | volume = 126 | issue = 6 | pages = 1065–77 | date = September 2006 | pmid = 16962654 | doi = 10.1016/j.cell.2006.08.032 | s2cid = 13452915 | doi-access = free }}</ref> These structures allow one to see the details of interactions of the ''[[Thermus thermophilus]]'' ribosome with [[mRNA]] and with [[tRNA]]s bound at classical ribosomal sites. Interactions of the ribosome with long mRNAs containing [[Shine-Dalgarno sequence]]s were visualized soon after that at 4.5–5.5&nbsp;[[Ångström|Å]] resolution.<ref>{{cite journal | vauthors = Yusupova G, Jenner L, Rees B, Moras D, Yusupov M | title = Structural basis for messenger RNA movement on the ribosome | journal = Nature | volume = 444 | issue = 7117 | pages = 391–4 | date = November 2006 | pmid = 17051149 | doi = 10.1038/nature05281 | bibcode = 2006Natur.444..391Y | s2cid = 4419198 }}</ref>

In 2011, the first complete atomic structure of the eukaryotic 80S ribosome from the yeast ''[[Saccharomyces cerevisiae]]''   was obtained by crystallography.<ref name="Ben-Shem-2011"/> The model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core. At the same time, the complete model of a eukaryotic 40S ribosomal structure in ''[[Tetrahymena thermophila]]'' was published and described the structure of the [[40S|40S subunit]], as well as much about the 40S subunit's interaction with [[eIF1]] during [[Translation (biology)|translation initiation]].<ref name="Rabl-2011"/> Similarly, the eukaryotic [[60S|60S subunit]] structure was also determined from ''[[Tetrahymena thermophila]]'' in complex with [[eIF6]].<ref name="Klinge-2011"/>