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# Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit | Nature

**URL:** https://www.nature.com/articles/23641

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Article
Published: 26 August 1999
Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit
Nenad Ban, Poul Nissen, Jeffrey Hansen, Malcolm Capel, Peter B. Moore & Thomas A. Steitz

Nature 
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 400, 
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841–847 (1999)Cite this article

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Abstract

We have calculated at 5.0 Å resolution an electron-density map of the large 50S ribosomal subunit from the bacterium Haloarcula marismortui by using phases derived from four heavy-atom derivatives, intercrystal density averaging and density-modification procedures. More than 300 base pairs of A-form RNA duplex have been fitted into this map, as have regions of non-A-form duplex, single-stranded segments and tetraloops. The long rods of RNA crisscrossing the subunit arise from the stacking of short, separate double helices, not all of which are A-form, and in many places proteins crosslink two or more of these rods. The polypeptide exit channel was marked by tungsten cluster compounds bound in one heavy-atom-derivatized crystal. We have determined the structure of the translation-factor-binding centre by fitting the crystal structures of the ribosomal proteins L6, L11 and L14, the sarcin–ricin loop RNA, and the RNA sequence that binds L11 into the electron density. We can position either elongation factor G or elongation factor Tu complexed with an aminoacylated transfer RNA and GTP onto the factor-binding centre in a manner that is consistent with results from biochemical and electron microscopy studies.

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References

Monro, R. E. Catalysis of peptide bond formation by 50S ribosomal subunits from Escherichia coli. J. Mol. Biol. 26, 147–151 (1967).

Article
 
CAS
 
Google Scholar

Wittmann-Liebold, B., in Structure, Function, and Genetics of Ribosomes (eds Hardesty, B. & Kramer, G.) 326–361 (Springer, New York, 1986).

Book
 
Google Scholar

Frank, J. et al. Amodel for protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376, 441–444 (1995).

Article
 
ADS
 
CAS
 
Google Scholar

Stark, H. et al. Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88, 19–28 (1997).

Article
 
CAS
 
Google Scholar

Milligan, R. A. & Unwin, P. N. T. Location of exit channel for nascent protein in 80S ribosome. Nature 319, 693–695 (1986).

Article
 
ADS
 
CAS
 
Google Scholar

Beckmann, R. et al. Alignment of conduits for the nascent polypeptide chain in the ribosome–Sec61 complex. Science 278, 2123–2128 (1997).

Article
 
ADS
 
CAS
 
Google Scholar

Liljas, A. in The Ribosome. Structure, Function & Evolution (eds Hill, W. E. et al.) 309–317 (Am. Soc. Microbiol., Washington DC, 1990).

Google Scholar

Capel, M. S. et al. Acomplete mapping of the proteins in the small ribosomal subunit of E. coli. Science 238, 1403–1406 (1987).

Article
 
ADS
 
CAS
 
Google Scholar

May, R. P., Nowotny, V., Nowotny, P., Voss, H. & Nierhaus, K. H. Inter-protein distances within the large subunit from Escherichia coli ribosomes. EMBO J. 11, 373–378 (1992).

Article
 
CAS
 
Google Scholar

Oakes, M. Henderson, E., Scheinman, A., Clark, M. & Lake, J. A. in Structure, Function and Genetics of Ribosomes (eds Hardesty, B. & Kramer, G.) 47–67 (Springer, New York, 1986).

Book
 
Google Scholar

Stoeffler, G. & Stoeffler-Meilicke, M. in Structure, Function, and Genetics of Ribosomes (eds Hardesty, B. & Kramer, G.) 28–46 (Springer, New York, 1986).

Book
 
Google Scholar

Ramakrishnan, A. & White, S. W. Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends Biochem. Sci. 23, 208–212 (1998).

Article
 
CAS
 
Google Scholar

Szewczak, A. A. & Moore, P. B. The sarcin/ricin loop, a modular RNA. J. Mol. Biol. 247, 81–98 (1995).

Article
 
CAS
 
Google Scholar

Correll, C. C. et al. Crystal structure of the ribosomal RNA loop essential for binding both elongation factors. Proc. Natl Acad. Sci. USA 95, 13436–13441 (1998).

Article
 
ADS
 
CAS
 
Google Scholar

Correll, C. C., Freeborn, B., Moore, P. B. & Steitz, T. A. Metals, motifs and recognition in the crystal structure of a 5S rRNA domain. Cell 91, 705–712 (1997).

Article
 
CAS
 
Google Scholar

Dallas, A. & Moore, P. B. The solution structure of the loop E/loop D regio of E. coli 5S rRNA. Structure 5, 1639–1653 (1997).

Article
 
CAS
 
Google Scholar

Wimberly, B. T., Guymon, R., McCutcheon, J. P., White, S. W. & Ramakrishnan, V. R. Adetailed view of a ribosomal active site: the structure of the L11–RNA complex. Cell 97, 491–502 (1999).

Article
 
CAS
 
Google Scholar

Conn, G. L., Draper, D. E., Lattman, E. E. & Gittis, A. G. Crystal structure of a conserved ribosomal protein RNA complex. Science 284, 1171–1174 (1999).

Article
 
ADS
 
CAS
 
Google Scholar

Agrawal, R. K., Penczek, P., Grassucci, R. A. & Frank, J. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA 95, 6134–6138 (1998).

Article
 
ADS
 
CAS
 
Google Scholar

Stark, H. et al. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403–406 (1997).

Article
 
ADS
 
CAS
 
Google Scholar

Ban, N. et al. A9 Å resolution X-ray crystallographic map of the large ribosomal subunit. Cell 93, 1105–1115 (1998).

Article
 
CAS
 
Google Scholar

Cowtan, K. D. An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994).

Google Scholar

Jones, T. A. in CCP4 Study Weekend, Molecular Replacement (eds Dodson, E. J., Glover, S. & Wolf, W.) 91–105 (SSRC, Daresbury Laboratory, Warrington, Cheshire, UK, 1992).

Google Scholar

Bernabeu, C. & Lake, J. A. Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: Immune mapping of the nascent chain. Proc. Natl Acad. Sci. USA 79, 3111–3115 (1982).

Article
 
ADS
 
CAS
 
Google Scholar

Kleywegt, G. J. & Jones, T. A. Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta. Crystallogr. D 53, 179–185 (1997).

Article
 
CAS
 
Google Scholar

Cate, J. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 (1996).

Article
 
ADS
 
CAS
 
Google Scholar

Jucker, F. M., Heus, H. A., Yip, P. F., Moors, E. H. M. & Pardi, A. Anetwork of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264, 968–980 (1996).

Article
 
CAS
 
Google Scholar

Stern, S., Powers, T., Changchien, L.-I. & Noller, H. F. RNA–proteins interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science 244, 783–790 (1989).

Article
 
ADS
 
CAS
 
Google Scholar

Golden, B. L., Ramakrishnan, V. & White, S. W. Ribosomal protein L6. Structural evidence of gene duplication from a primitive RNA binding protein. EMBO J. 12, 4901–4908 (1993).

Article
 
CAS
 
Google Scholar

Leffers, H., Kjems, J., Ostergaard, L., Larsen, N. & Garrett, R. A. Evolutionary relationships amongst archaebacteria: a comparative study of 23S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile, and a thermophilic mechanogen. J. Mol. Biol. 195, 43–61 (1987).

Article
 
CAS
 
Google Scholar

Leffers, H., Egeberg, J., Andersen, A., Christensen, T. & Garrett, R. A. Domain VI of Escherichia coli 23S ribosomal RNA structure, assembly and function. J. Mol. Biol. 204, 507–522 (1988).

Article
 
CAS
 
Google Scholar

Uchiumi, T., Sato, N., Wada, A. & Hachimori, A. Interaction of the sarcin/ricin domain of 23S ribosomal RNA with proteins L3 and L6. J. Biol. Chem. 274, 681–686 (1999).

Article
 
CAS
 
Google Scholar

Urlaub, H., Kruft, V., Bischof, O., Muller, E. C. & Wittmann-Liebold, B. Protein–rRNA binding features and their structural and functional implications in ribosomes as determined by crosslinking studies. EMBO J. 14, 4578–4588 (1995).

Article
 
CAS
 
Google Scholar

Davies, C., White, S. W. & Ramakrishnan, V. The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus. Structure 4, 55–66 (1996).

Article
 
CAS
 
Google Scholar

Walleczek, J., Schuler, D., Stoeffler-Meilicke, M., Brimacombe, R. & Stoeffler, G. Amodel for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome. EMBO J. 7, 3571–3576 (1988).

Article
 
CAS
 
Google Scholar

Nakagawa, A. et al. The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome. EMBO J. 18, 1459–1467 (1999).

Article
 
CAS
 
Google Scholar

Wilson, K. S. & Noller, H. H. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell 92, 131–139 (1998).

Article
 
CAS
 
Google Scholar

Aevarsson, A. et al. Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J. 13, 3669–3677 (1994).

Article
 
CAS
 
Google Scholar

Czworkowski, J., Wang, J., Steitz, T. A. & Moore, P. B. The crystal structure of elongation factor G complexed with GDP at 2.7 Å resolution. EMBO J. 13, 3661–3668 (1994).

Article
 
CAS
 
Google Scholar

Nissen, P. et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu and a GTP analog. Science 270, 1464–1472 (1995).

Article
 
ADS
 
CAS
 
Google Scholar

Moazed, D., Robertson, J. M. & Noller, H. F. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature 334, 362–364 (1988).

Article
 
ADS
 
CAS
 
Google Scholar

Traut, R. R. et al. in Structure, Function, and Genetics of Ribosomes (eds Hardesty, B. & Kramer, G.) 286–308 (Springer, New York, 1986).

Book
 
Google Scholar

Skold, S. E. Chemical crosslinking of elongation factor G to both subunits of the 70S ribosome from E. coli. Eur. J. Biochem. 127, 225–229 (1982).

Article
 
CAS
 
Google Scholar

Skold, S. E. Chemical crosslinking of elongation factor G to the 23S rRNA in 70S ribosomes from Escherichia coli. Nucleic Acids Res. 11, 4923–4932 (1983).

Article
 
CAS
 
Google Scholar

Nevskaya, N. et al. Structure of archaeal ribosomal protein L1 provides new insights into the RNA binding for the L1 protein family. J. Mol. Biol.(in the press).

von Bohlen, K. et al. Characterization and preliminary attempts for derivitization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 Å resolution. J. Mol. Biol. 222, 11–15 (1991).

Article
 
CAS
 
Google Scholar

Otwinowski, Z. in Data Collection and Processing (eds Sawyer, L., Isaacs, N. & Bailey, D.) 52–62 (SERC Daresbury Laboratory, Warrington, UK, 1993).

Google Scholar

Brünger, A. T. et al. Crystallography and NMR system (CNS): a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

Article
 
Google Scholar

Yeates, T. O. Detecting and overcoming crystal twinning. Methods Enzymol. 276, 344–358 (1997).

Article
 
CAS
 
Google Scholar

Abrahams, J. P. & Leslie, A. G. W. Methods used in the structural determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30–43 (1996).

Article
 
CAS
 
Google Scholar

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Acknowledgements

We thank E. Freeborn for biochemical support; R. Sweet for helping us with data collection at the National Synchrotron Light Source; and I.Tanaka, M. Garber and S. Al-Karadaghi for providing coordinates before publication. This investigation was supported by grants from NIH to T.A.S. and P.B.M. N.B. was a Damon Runyon-Walter Winchell Postdoctoral Fellow during part of this study, and P.N. is supported by the Danish Research Council. The coordinates of all identified RNA and protein structures have been deposited in the protein data bank with accession number IC04.

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Authors and Affiliations

Departments of Molecular Biophysics & Biochemistry Yale University, New Haven, 06520-8114, Connecticut, USA

Nenad Ban, Poul Nissen, Jeffrey Hansen & Thomas A. Steitz

Departments of Chemistry, Yale University, New Haven, 06520-8114, Connecticut, USA

Peter B. Moore & Thomas A. Steitz

Howard Hughes Medical Institute, New Haven, 06520-8114, Connecticut, USA

Nenad Ban, Jeffrey Hansen & Thomas A. Steitz

Department of Biology, Brookhaven National Laboratory, Upton, 11973, New York, USA

Malcolm Capel

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Ban, N., Nissen, P., Hansen, J. et al. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400, 841–847 (1999). https://doi.org/10.1038/23641

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Received
02 July 1999

Accepted
19 July 1999

Issue Date
26 August 1999

DOI
https://doi.org/10.1038/23641

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