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Chapter 2 : Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution
Authors:
Nenad Ban1,
Poul Nissen2,
Peter B. Moore3,
Thomas A. Steitz4
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Affiliations:
1: Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520;
2: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
3: Department of Chemistry and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520;
4: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, and Department of Chemistry, Yale University, New Haven, CT 06520
Content Type: Monograph
Publication Year:
2000
Category: Microbial Genetics and Molecular Biology
Book DOI:
10.1128/9781555818142
Chapter DOI:
10.1128/9781555818142.ch2
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Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, Page 1 of 2
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Abstract:
The ribonucleoproteins called ribosomes were discovered by cytologists in the mid-1950s, and by 1960 it was apparent that they catalyze protein synthesis. Ribosomes consume aminoacyl transfer RNAs, and the sequences of the proteins they produce are determined by those of the mRNAs with which they interact. The first ribosome crystals did not diffract to atomic resolution, but even if they had, it is uncertain what would have come of it in the short term; their analysis would have severely tested the crystallographic technology of the day. Heavy-atom cluster compounds are useful for phasing macromolecular diffraction patterns of large macromolecules at low resolution. The structure of an ordinary macromolecular crystal is solved when the experimental phases available are accurate to a resolution high enough so that an all-atom model of the molecule’s sequence can be fitted into the resulting electron density map. ESSENS can also be used to find less generic structures, such as the sarcin-ricin loop (SRL). The SRL is a critical part of the factor binding center, or GTPase center, of the large ribosomal subunit. A conformational change that moves L11 and its associated rRNA towards the putative factor binding site seems at least equally likely, and since there is no ribosomal material in the way to prevent it, that kind of motion is possible. In this connection, it is interesting to note that there is a substantial literature indicating that this part of the ribosome does indeed move during protein synthesis.
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
Figures
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution
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Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
/content/10.1128/9781555818142.chap2.fig2-1
Figure 1
Four versions of the electron density in a specific region of the large ribosomal subunit from H. marismortui. (A) The region as it appeared in the 9-Å-resolution map published in 1998 ( Ban et al., 1998 ) with an approximate molecular interpretation supplied. (B) The same region in a map computed with the phases available today, also to 9-Å resolution. (C) The region at the full resolution available today (5Å ). (D) The electron density expected if the atomic structure shown were the correct structure and if the resolution limit was in fact 5 Å . Panel D was computed by assuming a temperature factor of 80 Å2, which is appropriate for the H. marismortui crystals under investigation. Molecular models were prepared with the O program, and the illustrations were prepared with both O and RIBBONS ( Carson, 1991 ; Jones et al., 1991 ).
10.1128/9781555818142/fig2-1_thmb.gif
10.1128/9781555818142/fig2-1.gif
Figure 1
Four versions of the electron density in a specific region of the large ribosomal subunit from H. marismortui. (A) The region as it appeared in the 9-Å-resolution map published in 1998 ( Ban et al., 1998 ) with an approximate molecular interpretation supplied. (B) The same region in a map computed with the phases available today, also to 9-Å resolution. (C) The region at the full resolution available today (5Å ). (D) The electron density expected if the atomic structure shown were the correct structure and if the resolution limit was in fact 5 Å . Panel D was computed by assuming a temperature factor of 80 Å2, which is appropriate for the H. marismortui crystals under investigation. Molecular models were prepared with the O program, and the illustrations were prepared with both O and RIBBONS ( Carson, 1991 ; Jones et al., 1991 ).
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
/content/10.1128/9781555818142.chap2.fig2-2
Figure 2
A surface rendering of the large ribosomal subunit in the crown view. (Top) Stereo view of the subunit with EFG docked to the factor binding center. EF-G is the protein whose ribbon diagram is colored purple. (Bottom) The same view of the subunit with EF-G removed so that the factor binding center can be seen. In both panels, segments of helical RNA (white backbone) are inserted into the density in several places to guide the reader. Also inserted are ribbon diagrams for proteins L2, L6, L11, and L14 (yellow), the SRL (red backbone), two other segments of domain IV (blue backbone), and the thiostrepton binding segment of 23S rRNA (orange backbone). The position where L1 is seen in lower-resolution maps (see the text) is also indicated.
10.1128/9781555818142/fig2-2_thmb.gif
10.1128/9781555818142/fig2-2.gif
Figure 2
A surface rendering of the large ribosomal subunit in the crown view. (Top) Stereo view of the subunit with EFG docked to the factor binding center. EF-G is the protein whose ribbon diagram is colored purple. (Bottom) The same view of the subunit with EF-G removed so that the factor binding center can be seen. In both panels, segments of helical RNA (white backbone) are inserted into the density in several places to guide the reader. Also inserted are ribbon diagrams for proteins L2, L6, L11, and L14 (yellow), the SRL (red backbone), two other segments of domain IV (blue backbone), and the thiostrepton binding segment of 23S rRNA (orange backbone). The position where L1 is seen in lower-resolution maps (see the text) is also indicated.
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
/content/10.1128/9781555818142.chap2.fig2-3
Figure 3
Electron density in the L2 region. Electron density corresponding to the RNA binding domain of L2 is shown adjacent to the stem-loop that forms the bottom of the L1 stalk. It is clear that RNA can easily be distinguished from protein in these maps. (It should be noted that the atomic structures shown in this and all other figures have been fitted into the electron density by hand. No effort has been made to optimize these fits computationally. Furthermore, in every case, the protein structures used are those of homologues of the H. marismortui proteins in question, not the structures of the H. marismortui proteins themselves, none of which are known. Since the sequences of these homologues are not the same as those of the proteins they are being used to represent, some divergence between the structures used and the electron density into which they are fitted is to be expected.)
10.1128/9781555818142/fig2-3_thmb.gif
10.1128/9781555818142/fig2-3.gif
Figure 3
Electron density in the L2 region. Electron density corresponding to the RNA binding domain of L2 is shown adjacent to the stem-loop that forms the bottom of the L1 stalk. It is clear that RNA can easily be distinguished from protein in these maps. (It should be noted that the atomic structures shown in this and all other figures have been fitted into the electron density by hand. No effort has been made to optimize these fits computationally. Furthermore, in every case, the protein structures used are those of homologues of the H. marismortui proteins in question, not the structures of the H. marismortui proteins themselves, none of which are known. Since the sequences of these homologues are not the same as those of the proteins they are being used to represent, some divergence between the structures used and the electron density into which they are fitted is to be expected.)
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
/content/10.1128/9781555818142.chap2.fig2-4
Figure 4
L6 and the rRNA segments with which it interacts. The backbone structure of L6 is shown superimposed on the electron density assigned to it. Four rRNA segments interact with L6, and the SRL is on the far right.
10.1128/9781555818142/fig2-4_thmb.gif
10.1128/9781555818142/fig2-4.gif
Figure 4
L6 and the rRNA segments with which it interacts. The backbone structure of L6 is shown superimposed on the electron density assigned to it. Four rRNA segments interact with L6, and the SRL is on the far right.
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
/content/10.1128/9781555818142.chap2.fig2-5
Figure 5
Stereo views of a model for the interaction of EF-G and the EF-Tu•tRNA complex with the factor binding center of the large ribosomal subunit. (Top) A view of the model in the same orientation as in Fig. 2 , top. EF-G is shown in purple, the SRL is red, a helix is blue, helix 97 is yellow, and the thiostrepton RNA is orange. All ribosomal proteins are gray. (Middle) The same model as in the top panel, viewed from the top with the L11-rRNA assembly removed so that the interaction proposed to occur between the SRL and EF-G can be visualized. (Bottom) The same view as the middle panel with EF-G replaced by the EF-Tu•tRNA complex. The tRNA backbone is magenta.
10.1128/9781555818142/fig2-5_thmb.gif
10.1128/9781555818142/fig2-5.gif
Figure 5
Stereo views of a model for the interaction of EF-G and the EF-Tu•tRNA complex with the factor binding center of the large ribosomal subunit. (Top) A view of the model in the same orientation as in Fig. 2 , top. EF-G is shown in purple, the SRL is red, a helix is blue, helix 97 is yellow, and the thiostrepton RNA is orange. All ribosomal proteins are gray. (Middle) The same model as in the top panel, viewed from the top with the L11-rRNA assembly removed so that the interaction proposed to occur between the SRL and EF-G can be visualized. (Bottom) The same view as the middle panel with EF-G replaced by the EF-Tu•tRNA complex. The tRNA backbone is magenta.
Citation:
Ban N, Nissen P, Moore P, Steitz T.
2000.
Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution,
p 11-20.
In
Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed),
The Ribosome.
ASM Press, Washington, DC.
doi: 10.1128/9781555818142.ch2
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