Unveiling ribosomal structures: The final phases

Current Opinion in Structural Biology

Volumn 10, Issue 2, 2000, Pages 259-264

  Van Heel, Marin ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STRUCTURE; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; MOLECULAR WEIGHT; PRIORITY JOURNAL; REVIEW; RIBOSOME; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ESCHERICHIA COLI;

EID: 0034113895     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00077-4     Document Type: Review

References (43)

1. Dubochet J., Adrian M., Chang J.J., Homo J.C., Lepault J., McDowell A.W., Schultz P. Cryo-electron microscopy of vitrified specimens. Quart Rev Biophys. 21:1988;129-228.
2. Böttcher B., Wynne S.A., Crowther R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature. 386:1997;88-91.
3. Conway J., Cheng N., Wingfield P.T., Stahl S.J., Steven A.C. Visualisation of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature. 385:1997;91-94.
4. Stark H., Mueller F., Orlova E.V., Schatz M., Dube P., Erdemir T., Zemlin F., Brimacombe R., van Heel M. The 70S Escherichia coli ribosome at 23 Å resolution: fitting the ribosomal RNA. Structure. 3:1995;815-821.
5. Frank J., Zhu J., Penczek P., Li Y., Srivastava S., Verschoor A., Radermacher M., Grassucci R., Lata R.K., Agrawal R.K. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature. 376:1995;441-444.
6. van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy. 21:1987;111-124.
7. van Heel M., Orlova E.V., Harauz G., Stark H., Dube P., Zemlin F., Schatz M. Angular reconstitution: high resolution structures from uncrystallized macromolecules. Scanning Microscopy. 11:1997;195-210.
8. Stark H., Orlova E.V., Rinke-Appel J., Jünke N., Mueller F., Rodnina M., Wintermeyer W., Brimacombe R., van Heel M. Arrangement of the tRNAs in pre- and post-translocational ribosomes revealed by electron cryomicroscopy. Cell. 88:1997;19-28.
9. Stark H., Rodnina M.V., Rinke-Appel J., Brimacombe R., Wintermeyer W., van Heel M. Visualisation of elongation factor Tu on the Escherichia coli ribosome. Nature. 389:1997;403-406.
10. Agrawal R.K., Penczek P., Grassucci R.A., Frank J. Visualization of the elongation factor G on E. coli 70S ribosome: the mechanism of translation. Proc Natl Acad Sci USA. 95:1998;6134-6138. The first visualisation of elongation factor G (EF-G) on the ribosome using the antibiotic fusidic acid. The position of EF-G on the ribosome is in very good agreement with hydroxy-radical footprinting of EF-G GDP on the ribosome after translocation, prior to dissociation, frozen by the antibiotic fusidic acid.
11. ••].
12. Stark H., Rodnina M.V., Wieden H.J., van Heel M., Wintermeyer W. Large-scale movements of elongation factor G and extensive conformational changes of the ribosome during translocation. Cell. 100:2000;301-309. The antibiotic thiostrepton stalls the translocation process, such that it becomes possible to picture the pre-translocational and the post-translocational structures of the ribosome with elongation factor G (EF-G) bound. The post-translocational position of EF-G in the presence of thiostrepton differs from that seen in the presence of fusidic acid.
13. Agrawal R.K., Frank J. Structural studies of the translational apparatus. Curr Opin Struct Biol. 9:1999;215-221. A previous review in this journal series. A comparison of this review with my own review will reflect the speed of development towards increased resolution in just slightly over one year; cryo-electron microscopy resolution has improved from 15 Å to 7.5 Å.
14. Yonath A., Berkovitch-Yellin Z. Hollows, voids, gaps and tunnels in the ribosome. Curr Opin Struct Biol. 3:1993;175-181.
15. ••].
16. Harms J., Tocilj A., Levin I., Agmon I., Kölln I., Stark H., van Heel M., Cuff M., Schlünzen F., Bashan A.et al. Elucidating the structure of ribosomal particles: an interplay between electron-cryo-microscopy and X-ray crystallography. Structure. 7:1999;931-941. A description of some of the first phased ribosomal X-ray structures. The emphasis of the paper is more on the molecular replacement techniques applied and the work thus does not contain very explicit structural conclusions. Various structures were phased with the help of low-resolution cryo-electron microscopy maps.
17. Clemons W.M. Jr., May J.L., Wimberly B.T., McCutcheon J.P., Capel M.S., Ramakrishnan V. Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature. 400:1999;833-840. The very precise determination of the positions of all known small subunit proteins and a significant proportion of the 16S rRNA within the 30S ribosome densities.
18. Garrett R.A., Douthwaite S.R., Liljas A., Matheson A.T., Moore P.B., Noller H.F. The Ribosome; Structure, Function, Antibiotics, and Cellular Interactions. 1999;ASM Press, Washington, DC. The proceedings of the Helsingør International Ribosome meeting in June 1999 reflect the state-of-the-art in ribosomology at the turn of the millennium.
19. ••] is still controversial as it occupies densities hitherto assigned to the L7/L12 stalk in cryo-electron microscopy reconstructions.
20. ••].
21. ••].
22. Cate J.H., Yusupov M.M., Yusupova G.Z., Earnest T.N., Noller H.F. X-ray crystal structures of 70S ribosome functional complexes. Science. 285:1999;2095-2104. The first X-ray structure of the full ribosome at 7.8 Å resolution. The phasing of the map was assisted by an earlier cryo-electron microscopy 25 Å map of the 70S E. coli ribosome. Most interesting is the imaging of tRNAs (or fragments thereof) in the A and P sites. The study confirms the earlier cryo-electron microscopy results of Stark et al. [8], found at approximately 20 Å resolution, and refute the results of Agrawal et al. [42]. As discussed in the main text of this review, the protein components in the data are not well represented in the map.
23. Garret P. Mechanism of the ribosome. Nature. 400:1999;811-812. An editorial on the new X-ray structures of the ribosome.
24. Pennisi E. The race to the ribosome structure. Science. 285:1999;2048-2051. A nice editorial describing the dedication of the various researchers involved in the quest for the ribosome structure.
25. ••]. Liljas emphasises the importance for the field of making the low-resolution maps publicly available. It is otherwise virtually impossible to compare the results obtained by different groups, be it by X-ray crystallography or cryo-electron microscopy.
26. Green R., Puglisi J.D. The ribosome revealed. Nat Struct Biol. 6:1999;999-1003. A very detailed review of the recently determined X-ray structures of the ribosome.
27. •].
28. Hoffman D.W., Cameron C.S., Davies C., White S., Ramakrishnan V. Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy. J Mol Biol. 264:1996;1058-1071.
29. ••]; the density is also seen in cryo-electron microscopy maps of the 50S subunit from E. coli.
30. ••].
31. Kleywegt G.J., Brunger A.T. Checking your imagination: applications of the free R value. Structure. 4:1996;897-904.
32. Harauz G., van Heel M. Exact filters for general geometry three-dimensional reconstruction. Optik. 73:1986;146-156.
33. Met and fitting of L1 protein. J Mol Biol. 280:1998;103-115. This paper describes the 70S initiation complex at an intermediate 15 Å resolution level. The orientation of the P site tRNA has been corrected with respect to earlier work by this group and now confirms the results described in [8]. The fitting of the L1 protein must be interpreted with care, as no density has been reserved for the rRNA to which the L1 protein binds and the two domains of the L1 protein have not been fitted individually to account for the known conformational flexibility of the protein.
34. Orlova E.V., Dube P., Harris J.R., Beckman E., Zemlin F., Markl J., van Heel M. Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15Å resolution by electron cryomicroscopy and angular reconstitution. J Mol Biol. 271:1997;417-437.
35. Dube P., Wieske M., Stark H., Schatz M., Stahl J., Zemlin F., Lutsch G., van Heel M. The 80S rat liver ribosome at 25 Å resolution by electron microscopy and angular reconstruction. Structure. 6:1998;398-399. In spite of the much larger size of the 80S mammalian ribosome, its structural core overlaps very precisely with that of the bacterial ribosome. In particular, the large subunit can be aligned using well-known landmarks, such as the L1 protuberance, the A-site finger and the central protuberance. Once aligned, the exit channels overlap perfectly in these structures.
36. van Heel M., Schatz M., Orlova E. Correlation functions revisited. Ultramicroscopy. 46:1992;304-316.
37. Unge J., Berg A., Al-Kharadaghi S., Nikulin A., Nikonov S., Davydova N., Nevskaya N., Garber M., Liljas A. The crystal structure of ribosomal protein L22 from T. thermophilus: insights into the mechanism of erythromycin resistance. Structure. 6:1998;1577-1586. A paper on the structure of individual ribosomal proteins. Protein L22, which is deeply buried in the 50S subunit, may be one of the most difficult ones to fit in maps of the full 50S subunit.
38. Correll C.C., Wool I.G., Munishkin A. The two faces of the Escherichia coli 23S rRNA sarcin/ricin domain: the structure at 1.11 Å resolution. J Mol Biol. 292:1999;275-287. Amazing levels of resolution can sometimes be achieved for ribosomal components. X-ray crystallography or cryo-electron microscopy of full ribosomes or ribosomal subunits still have a long way to go to reach such levels of detail.
39. ••]. This model does not yet fully exploit all structural details visible in the 7.5 Å map, but it fits the entire length of both the 23S and the 5S rRNAs in the cryo-electron microscopy density.
40. •].
41. Stallings S.C., Moore P.B. The structure of an essential splicing element: stem loop IIa from yeast U2 snRNA. Structure. 5:1997;1173-1185.
42. Agrawal R.K., Penczek P., Grassucci R.A., Li Y., Leith A., Nierhaus K.H., Frank J. Direct visualization of A-, P- and E-site transfer RNAs in the E. coli ribosome. Science. 271:1996;1000-1002.
43. ••].