The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: Pattern fittings and the identification of a functional site
10.1073/pnas.96.25.14252
Crossref journal-article
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences (341)
Abstract

The electron density map of the small ribosomal subunit from Thermus thermophilus , constructed at 4.5 Å resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.

Bibliography

Tocilj, A., Schlünzen, F., Janell, D., Glühmann, M., Hansen, H. A. S., Harms, J., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., & Yonath, A. (1999). The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: Pattern fittings and the identification of a functional site. Proceedings of the National Academy of Sciences, 96(25), 14252–14257.

Authors 11
  1. Ante Tocilj (first)
  2. Frank Schlünzen (additional)
  3. Daniela Janell (additional)
  4. Marco Glühmann (additional)
  5. Harly A. S. Hansen (additional)
  6. Jörg Harms (additional)
  7. Anat Bashan (additional)
  8. Heike Bartels (additional)
  9. Ilana Agmon (additional)
  10. Francois Franceschi (additional)
  11. Ada Yonath (additional)
References 36 Referenced 95
  1. J Harms, A Tocilj, I Levin, I Agmon, H Stark, I Kolln, M van Heel, M Cuff, F Schlunzen, A Bashan, et al. Structure Fold Des 7, 931–941 (1999). (10.1016/S0969-2126(99)80120-8) / Structure Fold Des by Harms J (1999)
  2. I S Gabashivili, R K Agrawal, R Grassucci, J Frank J Mol Biol 286, 1285–1291 (1999). (10.1006/jmbi.1999.2538) / J Mol Biol by Gabashivili I S (1999)
  3. R Wang, R W Alexander, M VanLoock, S Vladimirov, Y Bukhtiyarov, S C Harvey, B S Cooperman J Mol Biol 286, 521–540 (1999). (10.1006/jmbi.1998.2493) / J Mol Biol by Wang R (1999)
  4. W E Tapprich, W E Hill Proc Natl Acad Sci USA 83, 556– 560 (1986). (10.1073/pnas.83.3.556) / Proc Natl Acad Sci USA by Tapprich W E (1986)
  5. A Yonath, C Glotz, H S Gewitz, K Bartels, K von Boehlen, I Makowski, H G Wittmann J Mol Biol 203, 831–833 (1988). (10.1016/0022-2836(88)90216-1) / J Mol Biol by Yonath A (1988)
  6. S D Trakhanov, M M Yusupov, S C Agalarov, M B Garber, S N Ryazantsev, S V Tischenko, U A Shirokov FEBS Lett 220, 319–322 (1987). (10.1016/0014-5793(87)80838-4) / FEBS Lett by Trakhanov S D (1987)
  7. N Ban, B Freeborn, P Nissen, P Penczek, R A Grassucci, R Sweet, F Frank, P Moore, T Steitz Cell 93, 1105–1115 (1998). (10.1016/S0092-8674(00)81455-5) / Cell by Ban N (1998)
  8. B Dawson Acta Crystallogr 6, 113–126 (1953). (10.1107/S0365110X53000466) / Acta Crystallogr by Dawson B (1953)
  9. A Yonath, J Harms, H A Hansen, A Bashan, F Schlunzen, I Levin, I Koelln, A Tocilj, I Agmon, M Peretz, et al. Acta Crystallogr A 54, 945–955 (1998). (10.1107/S010876739800991X) / Acta Crystallogr A by Yonath A (1998)
  10. A Zamir, R Miskin, D Elson J Mol Biol 60, 347–364 (1971). (10.1016/0022-2836(71)90299-3) / J Mol Biol by Zamir A (1971)
  11. Auerbach T. Pioletti M. Avila H. Anagnostopoulos K. Weinstein S. Franceschi F. & Yonath A. (1999) Biomol. Struct. Dyn. in press.
  12. H Stark, F Mueller, E V Orlova, M Schatz, P Dube, T Erdemir, F Zemlin, R Brimacombe, M van Heel Structure (London) 3, 815–821 (1995). (10.1016/S0969-2126(01)00216-7) / Structure (London) by Stark H (1995)
  13. J Frank, J Zhu, P Penczek, Y Li, S Srivastava, A Verschoor, M Radermacher, R Grassucci, A R Lata, R K Agrawal Nature (London) 376, 441–444 (1995). (10.1038/376441a0) / Nature (London) by Frank J (1995)
  14. G Stöffler, M Stöffler-Meilicke Structure, Function and Genetics of Ribosomes, eds B Hardesty, G Kramer (Springer, Heidelberg), pp. 28–46 (1986). (10.1007/978-1-4612-4884-2_2) / Structure, Function and Genetics of Ribosomes by Stöffler G (1986)
  15. M I Oakes, M W Clark, E Henderson, J A Lake Proc Natl Acad Sci USA 83, 275–279 (1986). (10.1073/pnas.83.2.275) / Proc Natl Acad Sci USA by Oakes M I (1986)
  16. P B Moore, M S Capel, M Kjeldgaard, D M Engelman Structure, Function and Genetics of Ribosomes, eds B Hardesty, G Kramer (Springer, Heidelberg), pp. 87–100 (1985). / Structure, Function and Genetics of Ribosomes by Moore P B (1985)
  17. C Merryman, D Moazed, J McWhirter, H F Noller J Mol Biol 285, 97–105 (1999). (10.1006/jmbi.1998.2242) / J Mol Biol by Merryman C (1999)
  18. A Malhotra, S C Harvey J Mol Biol 240, 308–340 (1994). (10.1006/jmbi.1994.1448) / J Mol Biol by Malhotra A (1994)
  19. F Müller, R Brimacombe J Mol Biol 271, 524–544 (1997). (10.1006/jmbi.1997.1210) / J Mol Biol by Müller F (1997)
  20. A Liljas, S Al-Karadaghi Nat Struct Biol 4, 767–771 (1997). (10.1038/nsb1097-767) / Nat Struct Biol by Liljas A (1997)
  21. V Ramakrishnan, S W White Trends Biochem Sci 3, 208–212 (1998). (10.1016/S0968-0004(98)01214-6) / Trends Biochem Sci by Ramakrishnan V (1998)
  22. J Nyborg, P Nissen, M Kjeldgaard, S Thirup, G Polekhina, B F C Clark, L Reshetnikova Trends Biochem Sci 21, 81–82 (1996). (10.1016/S0968-0004(96)30008-X) / Trends Biochem Sci by Nyborg J (1996)
  23. F Schlünzen, I Koelln, D Janell, M Gluehmann, I Levin, A Bashan, J Harms, H Bartels, T Auerbach, Pioletti, et al. J Synth Radiation 6, 928–941 (1999). (10.1107/S0909049599006664) / J Synth Radiation by Schlünzen F (1999)
  24. S Weinstein, W Jahn, C Glotz, F Schluenzen, I Levin, D Janell, J Harms, I Kolln, H A S Mansen, M Gluehmann, et al. J Struct Biol 127, 141–151 (1999). (10.1006/jsbi.1999.4135) / J Struct Biol by Weinstein S (1999)
  25. Z Otwinowski, W Minor Methods Enzymol 276, 307–326 (1997). (10.1016/S0076-6879(97)76066-X) / Methods Enzymol by Otwinowski Z (1997)
  26. Acta Crystallogr D 50, 760–763 (1994). (10.1107/S0907444994003112) / Acta Crystallogr D (1994)
  27. E La Fortelle, G de Bricogne Methods Enzymol 276, 472–494 (1997). (10.1016/S0076-6879(97)76073-7) / Methods Enzymol by La Fortelle E (1997)
  28. J P Abrahams, A G W Leslie Acta Crystallogr D 52, 30–42 (1996). (10.1107/S0907444995008754) / Acta Crystallogr D by Abrahams J P (1996)
  29. T A Jones, J-Y Zou, S W Cowan, M Kjeldgaard Acta Crystallogr A 47, 110–119 (1991). (10.1107/S0108767390010224) / Acta Crystallogr A by Jones T A (1991)
  30. M Carson J Appl Crystallogr 24, 958–961 (1991). (10.1107/S0021889891007240) / J Appl Crystallogr by Carson M (1991)
  31. C Wolberger, Y Ding, M Ptashne, S H Harrison Nature (London) 335, 789–795 (1988). (10.1038/335789a0) / Nature (London) by Wolberger C (1988)
  32. J Jaeger, T Restle, T A Steitz EMBO J 17, 4535–4542 (1998). (10.1093/emboj/17.15.4535) / EMBO J by Jaeger J (1998)
  33. S Price, S Cusack, F Borel, C Berthetcolominas, R Leberman FEBS Lett 324, 167–170 (1993). (10.1016/0014-5793(93)81386-E) / FEBS Lett by Price S (1993)
  34. B Golden, A R Gooding, E R Podell, T A Cech Science 282, 259–264 (1998). (10.1126/science.282.5387.259) / Science by Golden B (1998)
  35. W M Clemons, J L May, B T Wimberly, J P McCutcheon, M S Capel, V Ramakrishnan Nature (London) 400, 833–840 (1999). (10.1038/23631) / Nature (London) by Clemons W M (1999)
  36. Ban N. Nissen P. Hansen J. Capel M. Moore P. B. & Steitz T. A. Nature (London) 400 841–847. (10.1038/23641)
Dates
Type When
Created 23 years ago (July 26, 2002, 10:35 a.m.)
Deposited 3 years, 2 months ago (June 7, 2022, 12:16 a.m.)
Indexed 1 month, 2 weeks ago (July 11, 2025, 6:49 a.m.)
Issued 25 years, 8 months ago (Dec. 7, 1999)
Published 25 years, 8 months ago (Dec. 7, 1999)
Published Online 25 years, 8 months ago (Dec. 7, 1999)
Published Print 25 years, 8 months ago (Dec. 7, 1999)
Funders 0

None

@article{Tocilj_1999, title={The small ribosomal subunit from Thermus thermophilus at 4.5 Å resolution: Pattern fittings and the identification of a functional site}, volume={96}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.96.25.14252}, DOI={10.1073/pnas.96.25.14252}, number={25}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Tocilj, Ante and Schlünzen, Frank and Janell, Daniela and Glühmann, Marco and Hansen, Harly A. S. and Harms, Jörg and Bashan, Anat and Bartels, Heike and Agmon, Ilana and Franceschi, Francois and Yonath, Ada}, year={1999}, month=dec, pages={14252–14257} }