Visualization of the eEF2-80S Ribosome Transition-State Complex by Cryo-Electron Microscopy

Journal of Molecular Biology

Volumn 382, Issue 1, 2008, Pages 179-187

  Sengupta, Jayati ^a   Nilsson, Jakob ^b   Gursky, Richard ^c   Kjeldgaard, Morten ^b   Nissen, Poul ^b   Frank, Joachim ^c,d  

^a WADSWORTH CENTER   (United States)

^b AARHUS UNIVERSITY   (Denmark)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

AlF4 ; GDP; GTPase; ribosome; translocation

Indexed keywords

ALUMINUM DERIVATIVE; ALUMINUM TETRAFLUORIDE; ELONGATION FACTOR 2; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATE; RIBOSOME RNA; RNA 18S;

ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; HYDROLYSIS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RIBOSOME SUBUNIT; RNA TRANSPORT; STRUCTURE ANALYSIS;

EID: 49349091956     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.07.004     Document Type: Article

References (36)

1. Frank J., Gao H., Sengupta J., Gao N., and Taylor D.J. The process of mRNA-tRNA translocation. Proc. Natl Acad. Sci. USA 104 (2007) 19671-19678
2. AEvarsson A., Brazhnikov E., Garber M., Zheltonosova J., Chirgadze Y., al-Karadaghi S., et al. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J. 13 (1994) 3669-3677
3. Czworkowski J., Wang J., Steitz T.A., and Moore P.B. The crystal structure of elongation factor G complexed with GDP, at 2.7 Å resolution. EMBO J. 13 (1994) 3661-3668
4. Jorgensen R., Ortiz P.A., Carr-Schmid A., Nissen P., Kinzy T.G., and Andersen G.R. Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Nat. Struct. Biol. 10 (2003) 379-385
5. Frank J., and Agrawal R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406 (2000) 318-322
6. Ermolenko D.N., Majumdar Z.K., Hickerson R.P., Spiegel P.C., Clegg R.M., and Noller H.F. Observation of intersubunit movement of the ribosome in solution using FRET. J. Mol. Biol. 370 (2007) 530-540
7. Spahn C.M., Gomez-Lorenzo M.G., Grassucci R.A., Jorgensen R., Andersen G.R., Beckmann R., et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23 (2004) 1008-1019
8. Taylor D.J., Nilsson J., Merrill A.R., Andersen G.R., Nissen P., and Frank J. Structures of modified eEF2 80S ribosome complexes reveal the role of GTP hydrolysis in translocation. EMBO J. 26 (2007) 2421-2431
9. Agrawal R.K., Penczek P., Grassucci R.A., and Frank J. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA 95 (1998) 6134-6138
10. Wieden H.J., Gromadski K., Rodnin D., and Rodnina M.V. Mechanism of elongation factor (EF)-Ts-catalyzed nucleotide exchange in EF-Tu. Contribution of contacts at the guanine base. J. Biol. Chem. 277 (2002) 6032-6036
11. Savelsbergh A., Katunin V.I., Mohr D., Peske F., Rodnina M.V., and Wintermeyer W. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol. Cell 11 (2003) 1517-1523
12. Rodnina M.V., Savelsbergh A., and Wintermeyer W. Dynamics of translation on the ribosome: molecular mechanics of translocation. FEMS Microbiol. Rev. 23 (1999) 317-333
13. Rodnina M.V., Savelsbergh A., Katunin V.I., and Wintermeyer W. Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385 (1997) 37-41
14. Wilden B., Savelsbergh A., Rodnina M.V., and Wintermeyer W. Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome. Proc. Natl Acad. Sci. USA 103 (2006) 13670-13675
15. Wintermeyer W., Peske F., Beringer M., Gromadski K.B., Savelsbergh A., and Rodnina M.V. Mechanisms of elongation on the ribosome: dynamics of a macromolecular machine. Biochem. Soc. Trans. 32 (2004) 733-737
16. Sprang S.R. G proteins, effectors and GAPs: structure and mechanism. Curr. Opin. Struct. Biol. 7 (1997) 849-856
17. Wittinghofer A. Signaling mechanistics: aluminum fluoride for molecule of the year. Curr. Biol. 7 (1997) R682-R685
18. Nilsson J., Sengupta J., Gursky R., Nissen P., and Frank J. Comparison of fungal 80S ribosomes by cryo-EM reveals diversity in structure and conformation of rRNA expansion segments. J. Mol. Biol. 369 (2007) 429-438
19. Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., and Frank J. Locking and unlocking of ribosomal motions. Cell 114 (2003) 123-134
20. Vetter I.R., and Wittinghofer A. The guanine nucleotide-binding switch in three dimensions. Science 294 (2001) 1299-1304
21. Abel K., Yoder M.D., Hilgenfeld R., and Jurnak F. An alpha to beta conformational switch in EF-Tu. Structure 4 (1996) 1153-1159
22. Liljas A., AEvarsson A., al-Karadaghi S., Garber M., Zheltonosova J., and Brazhnikov E. Crystallographic studies of elongation factor G. Biochem. Cell Biol. 73 (1995) 1209-1216
23. Polekhina G., Thirup S., Kjeldgaard M., Nissen P., Lippmann C., and Nyborg J. Helix unwinding in the effector region of elongation factor EF-Tu-GDP. Structure 4 (1996) 1141-1151
24. Connell S.R., Takemoto C., Wilson D.N., Wang H., Murayama K., Terada T., et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell 25 (2007) 751-764
25. Valle M., Zavialov A., Li W., Stagg S.M., Sengupta J., Nielsen R.C., et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10 (2003) 899-906
26. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., and Noller H.F. Crystal structure of the ribosome at 5.5 Å resolution. Science 292 (2001) 883-896
27. Spahn C.M., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., and Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions. Cell 107 (2001) 373-386
28. Ogle J.M., and Ramakrishnan V. Structural insights into translational fidelity. Annu. Rev. Biochem. 74 (2005) 129-177
29. Wimberly B.T., Brodersen D.E., Clemons Jr. W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., et al. Structure of the 30S ribosomal subunit. Nature 407 (2000) 327-339
30. Yassin A., Fredrick K., and Mankin A.S. Deleterious mutations in small subunit ribosomal RNA identify functional sites and potential targets for antibiotics. Proc. Natl Acad. Sci. USA 102 (2005) 16620-16625
31. Spirin A.S. Ribosome as a molecular machine. FEBS Lett. 514 (2002) 2-10
32. Bretscher M.S. Translocation in protein synthesis: a hybrid structure model. Nature 218 (1968) 3
33. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., and Leith A. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116 (1996) 190-199
34. Valle M., Sengupta J., Swami N.K., Grassucci R.A., Burkhardt N., Nierhaus K.H., et al. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21 (2002) 3557-3567
35. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., Sect. A: Found. Crystallogr. 47(Pt 2) (1991) 110-119
36. Carson M. Ribbons 2.0. J. Appl. Crystallogr. 24 (1991) 958-961