Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1,2,3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure–function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure–function relationships in ribozymes.
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Nakane, T. et al. Single-particle cryo-EM at atomic resolution. Nature 587, 152–156 (2020).
Yip, K. M., Fischer, N., Paknia, E., Chari, A. & Stark, H. Atomic-resolution protein structure determination by cryo-EM. Nature 587, 157–161 (2020).
Zhang, K., Pintilie, G. D., Li, S., Schmid, M. F. & Chiu, W. Resolving individual atoms of protein complex by cryo-electron microscopy. Cell Res. 30, 1136–1139 (2020).
Kruger, K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31, 147–157 (1982).
Cech, T. R. The RNA worlds in context. Cold Spring Harb. Perspect. Biol. 4, a006742 (2012).
Cech, T. R. & Steitz, J. A. The noncoding RNA revolution—trashing old rules to forge new ones. Cell 157, 77–94 (2014).
Zhang, H. & Keane, S. C. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. Wiley Interdiscip. Rev. RNA 10, e1541 (2019).
Zhang, J. & Ferré-D’Amaré, A. R. New molecular engineering approaches for crystallographic studies of large RNAs. Curr. Opin. Struct. Biol. 26, 9–15 (2014).
Zhang, K. et al. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nat. Commun. 10, 5511 (2019).
Kappel, K. et al. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat. Methods 17, 699–707 (2020).
Cech, T. R. Ribozymes, the first 20 years. Biochem. Soc. Trans. 30, 1162–1166 (2002).
Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 (1996).
Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282, 259–264 (1998).
Guo, F., Gooding, A. R. & Cech, T. R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol. Cell 16, 351–362 (2004).
Juneau, K., Podell, E., Harrington, D. J. & Cech, T. R. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA–solvent interactions. Structure 9, 221–231 (2001).
Piccirilli, J. A., Vyle, J. S., Caruthers, M. H. & Cech, T. R. Metal ion catalysis in the Tetrahymena ribozyme reaction. Nature 361, 85–88 (1993).
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J. & Strobel, S. A. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45–50 (2004).
Golden, B. L., Kim, H. & Chase, E. Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12, 82–89 (2005).
Shan, S., Yoshida, A., Sun, S., Piccirilli, J. A. & Herschlag, D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc. Natl Acad. Sci. USA 96, 12299–12304 (1999).
Stahley, M. R. & Strobel, S. A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309, 1587–1590 (2005).
Steitz, T. A. & Steitz, J. A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498–6502 (1993).
Forconi, M., Piccirilli, J. A. & Herschlag, D. Modulation of individual steps in group I intron catalysis by a peripheral metal ion. RNA 13, 1656–1667 (2007).
Beaudry, A. A. & Joyce, G. F. Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron. Biochemistry 29, 6534–6539 (1990).
Benz-Moy, T. L. & Herschlag, D. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry 50, 8733–8755 (2011).
Doherty, E. A. & Doudna, J. A. Ribozyme structures and mechanisms. Annu. Rev. Biophys. Biomol. Struct. 30, 457–475 (2001).
Joyce, G. F., van der Horst, G. & Inoue, T. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res. 17, 7879–7889 (1989).
Lehnert, V., Jaeger, L., Michel, F. & Westhof, E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol. 3, 993–1009 (1996).
Russell, R. et al. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. J. Mol. Biol. 363, 531–544 (2006).
Cate, J. H. et al. RNA tertiary structure mediation by adenosine platforms. Science 273, 1696–1699 (1996).
Cate, J. H., Hanna, R. L. & Doudna, J. A. A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4, 553–558 (1997).
Shoffner, G. M., Wang, R., Podell, E., Cech, T. R. & Guo, F. In crystallo selection to establish new RNA crystal contacts. Structure 26, 1275–1283.e3 (2018).
Pintilie, G. et al. Measurement of atom resolvability in cryo-EM maps with Q-scores. Nat. Methods 17, 328–334 (2020).
Shi, X. et al. Roles of long-range tertiary interactions in limiting dynamics of the Tetrahymena group I ribozyme. J. Am. Chem. Soc. 136, 6643–6648 (2014).
Downs, W. D. & Cech, T. R. A tertiary interaction in the Tetrahymena intron contributes to selection of the 5′ splice site. Genes Dev. 8, 1198–1211 (1994).
Zarrinkar, P. P. & Williamson, J. R. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme. Nucleic Acids Res. 24, 854–858 (1996).
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).
Wang, J. F., Downs, W. D. & Cech, T. R. Movement of the guide sequence during RNA catalysis by a group I ribozyme. Science 260, 504–508 (1993).
Lipchock, S. V. & Strobel, S. A. A relaxed active site after exon ligation by the group I intron. Proc. Natl Acad. Sci. USA 105, 5699–5704 (2008).
Karbstein, K. & Herschlag, D. Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function. Proc. Natl Acad. Sci. USA 100, 2300–2305 (2003).
Karbstein, K., Lee, J. & Herschlag, D. Probing the role of a secondary structure element at the 5′- and 3′-splice sites in group I intron self-splicing: the Tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing. Biochemistry 46, 4861–4875 (2007).
Shi, X., Mollova, E. T., Pljevaljcić, G., Millar, D. P. & Herschlag, D. Probing the dynamics of the P1 helix within the Tetrahymena group I intron. J. Am. Chem. Soc. 131, 9571–9578 (2009).
Shan, S., Kravchuk, A. V., Piccirilli, J. A. & Herschlag, D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry 40, 5161–5171 (2001).
Shan, S. O. & Herschlag, D. An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction. RNA 6, 795–813 (2000).
Sjögren, A. S., Pettersson, E., Sjöberg, B. M. & Strömberg, R. Metal ion interaction with cosubstrate in self-splicing of group I introns. Nucleic Acids Res. 25, 648–653 (1997).
Weinstein, L. B., Jones, B. C., Cosstick, R. & Cech, T. R. A second catalytic metal ion in group I ribozyme. Nature 388, 805–808 (1997).
Forconi, M., Lee, J., Lee, J. K., Piccirilli, J. A. & Herschlag, D. Functional identification of ligands for a catalytic metal ion in group I introns. Biochemistry 47, 6883–6894 (2008).
Hougland, J. L., Kravchuk, A. V., Herschlag, D. & Piccirilli, J. A. Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol. 3, e277 (2005).
Zaug, A. J., Grosshans, C. A. & Cech, T. R. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry 27, 8924–8931 (1988).
Kladwang, W., Hum, J. & Das, R. Ultraviolet shadowing of RNA can cause significant chemical damage in seconds. Sci. Rep. 2, 517 (2012).
Rajagopal, J., Doudna, J. A. & Szostak, J. W. Stereochemical course of catalysis by the Tetrahymena ribozyme. Science 244, 692–694 (1989).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Chen, M. et al. Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods 14, 983–985 (2017).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019).
Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Kappel, K. et al. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nat. Methods 15, 947–954 (2018).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
Frederiksen, J. K., Li, N. S., Das, R., Herschlag, D. & Piccirilli, J. A. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. RNA 18, 1123–1141 (2012).
Strauss-Soukup, J. K. & Strobel, S. A. A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme. J. Mol. Biol. 302, 339–358 (2000).
Ortoleva-Donnelly, L., Szewczak, A. A., Gutell, R. R. & Strobel, S. A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4, 498–519 (1998).
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
Green, R. & Szostak, J. W. In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sunY group I self-splicing intron. J. Mol. Biol. 235, 140–155 (1994).
Karbstein, K., Tang, K. H. & Herschlag, D. A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect. RNA 10, 1730–1739 (2004).
Tanner, M. A., Anderson, E. M., Gutell, R. R. & Cech, T. R. Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. RNA 3, 1037–1051 (1997).
Tanner, M. A. & Cech, T. R. Joining the two domains of a group I ribozyme to form the catalytic core. Science 275, 847–849 (1997).
Ikawa, Y., Yoshimura, T., Hara, H., Shiraishi, H. & Inoue, T. Two conserved structural components, A-rich bulge and P4 XJ6/7 base-triples, in activating the group I ribozymes. Genes Cells 7, 1205–1215 (2002).
Ikawa, Y., Naito, D., Shiraishi, H. & Inoue, T. Structure–function relationships of two closely related group IC3 intron ribozymes from Azoarcus and Synechococcus pre-tRNA. Nucleic Acids Res. 28, 3269–3277 (2000).
Michel, F., Ellington, A. D., Couture, S. & Szostak, J. W. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347, 578–580 (1990).
Szewczak, A. A. et al. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proc. Natl Acad. Sci. USA 96, 11183–11188 (1999).
Rangan, P., Masquida, B., Westhof, E. & Woodson, S. A. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl Acad. Sci. USA 100, 1574–1579 (2003).
Green, R., Ellington, A. D. & Szostak, J. W. In vitro genetic analysis of the Tetrahymena self-splicing intron. Nature 347, 406–408 (1990).
Mitchell, D., III, Jarmoskaite, I., Seval, N., Seifert, S. & Russell, R. The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations. J. Mol. Biol. 425, 2670–2686 (2013).
We thank R. N. Sengupta, D. Herschlag and I. Zheludev for discussions. Cryo-EM data were collected at SLAC and Stanford, and processed at SLAC, Stanford and Duyu High Performance Computing Center in Sichuan University. This work was supported by the National Institutes of Health (P41GM103832, R01GM079429, P01AI120943, and S10OD021600 to W.C.; R35GM112579 and R21AI145647 to R.D.); National Science Foundation (DGE-114747 to K.K. and DGE-1656518 to R.R.); Gabilan Stanford Graduate Fellowship to K.K.; Sichuan University start-up funding 20822041D4057 and Natural Science Foundation of China (NSFC82041016 and 32070049 to Z.S). We thank N. Lawless for manuscript editing.
The authors declare no competing interests.
Peer review information Nature thanks Thomas Cech, Amedee des Georges and Andrej Lupták for their contribution to the peer review of this work. Peer reviewer reports are available.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data figures and tables
Related to Fig. 1. a, Single-particle pipeline yields the final cryo-EM reconstruction with the corresponding angular distribution and local resolution map. The local resolution map shows more flexibility and lower resolution in the 4-nt bulge that connects stem P2.1 and P13, and towards the end of stem P6 and P9.2. b, FSC curve shows 3.1 Å resolution according to the 0.143 cutoff. c, Cryo-EM B factor64, which relates the number of particles to the map resolution attributed to cumulative experimental and computational factors that affect the final reconstruction.
Extended Data Fig. 2 Focused 3D classification of apo L-21 ScaI ribozyme reveals local conformational dynamics.
The regions of low local resolution, P9.2 (blue), P9.2–P9.1–P13 (orange) and P13 (green), were extracted. Focused 3D classification was performed and different classes were superimposed to show rotational and translational motions on P9.2 (left), P9.2–P9.1–P13 (middle) and P13 (right).
Extended Data Fig. 3 Q-score analyses of cryo-EM maps and models of both the apo L-21 and holo L-16 ScaI ribozymes.
Related to Fig. 1. a, Q-score analyses per residue of the apo L-21 (grey) and holo L-16 (blue) ScaI ribozyme cryo-EM models and maps. Black dashed line indicates average Q-score from nucleic acid cryo-EM models and maps at 3.1 Å resolution in the PDB. b, Cryo-EM model of apo L-21 ScaI ribozyme coloured according to Q-score per residue. Dashed boxes (black, blue and green) correspond to regions in the cryo-EM model with low Q-scores in a.
Extended Data Fig. 4 Detailed tertiary interactions in the core region of the apo L-21 ScaI ribozyme.
a–f, The P5–J5/5a–L9 region has a highly structured J5–5a junction in previous structures12,15. The cryo-EM structure shows tertiary interactions of C197 (a), C124 and A125 (b), G126, A324 and A325 (d, e) and G327 (f) in the minor groove of P5. g–k, Previous studies have shown that A183 and A184 in the A-rich bulge of the metal core, U259 and C260 from J6/J7 and U305 from J8/J7 are conserved and essential for catalytic site formation and splicing reactions65,66,67,68,69,70,71. The cryo-EM structure shows that U259 (h), C260 (i) and U305 (j, k) stack continuously and interact with P4 base triples. k, U168 from P5c stacks on the A-rich bulge and interacts with P4 in the minor groove, while pairing with G188 in P5a. l, The Hoogsteen base triple U277–A97–U300 is essential for substrate helix recognition72. m–q, In the P3–J3/4–P6–J7/3 region, the A-rich J3/4 and J7/3 were previously found to interact with P6 in the Azoarcus ribozyme17,73. Base triples formed by J3/4 were critical for catalysis65,70,71,74, and alterations in these regions result in RNA misfolding28,75. In the cryo-EM structure, A104 and A105 form A-minor interactions with P6, whereas A103 and A104 join A269 and A270 from J7/3 to form an adenosine cluster (m, n). The proposed A103–U271 reverse-Hoogsteen pair is not found; instead we observed a noncanonical A103–A270 pair74. p, q, The previously observed A-platform of A218–A219 is disrupted in the cryo-EM structure with P3 present12,29. A218 forms two A-minor interactions with C102–G272 and U273–U101 from P3, which also supports the conservation of this C–G pair in group Ib introns74. Black dashed lines indicate hydrogen bonds. The cryo-EM maps of all subpanels are visualized at 1σ threshold except for c, g, o (1.5σ).
Extended Data Fig. 5 Comparison between the previous 3.8 Å crystal structure of the mutated Tetrahymena ribozyme catalytic core (green) and the cryo-EM structure of the wild-type apo L-21 ScaI ribozyme construct (grey) shows minor differences.
Related to Extended Data Fig. 4. The overall r.m.s.d. for the catalytic core region (stem P3–P9) is 6.6 Å. a, The same view of the P5–J5/5a–P9 region as in Extended Data Fig. 4c. The nucleotide conformations generally agree well between two models; three mutations (U322C, U323G and U326A) are not involved in tertiary interactions. The r.m.s.d. for this region is 4.9 Å. b, The same view of the P4–P5a–J6/7–J8/7 region as in Extended Data Fig. 4g. In the crystal structure, U259A is slightly moved away from the G108–C213 base pair and disrupts this base triple interaction. A210G is moved far away from the wild-type position of A210, because there is no A46 in stem P2 to interact with in the crystal structure. The very top base quartet is much more compact in the cryo-EM structure compared to the crystal structure, probably owing to the presence of the peripheral domain that wraps around the catalytic core to make it more compact. The r.m.s.d. for this region is 5.7 Å. c, The same view of the P3–J3/4–P6–J7/3 region as in Extended Data Fig. 4o. The overall nucleotide conformations agree very well between the two models, except that A269G and A270 in the crystal structure are completely moved away and disrupt their interactions with A103, which is observed in the cryo-EM structure. The r.m.s.d. for this region is 1.7 Å. d, The same view as in Extended Data Fig. 4l. U277C disrupts the U277–A97–U300 base triple. The r.m.s.d. for this base triple is 2.7 Å. See also Supplementary Table 1.
Extended Data Fig. 6 Superposition of the apo L-21 ScaI ribozyme cryo-EM structure (grey) with previous crystal structures of the truncated and/or mutated Tetrahymena ribozyme, other group I introns and 5S rRNA loop E show global and local structural similarities.
a–d, Overlays of the cryo-EM structure (grey) with the Tetrahymena ribozyme P4–P6 Delta C209 (a; blue, PDB 1HR2); the mutated Tetrahymena ribozyme P3–P9 (b; green, PDB 1X8W); the Azoarcus ribozyme (c; violet, PDB 1U6B) and the phage Twort ribozyme (d; yellow, PDB 1Y0Q). e, P5c region of the wild type P4–P6 crystal structure (blue, PDB 1GID). f, 5S rRNA loop E crystal structure (red, PDB 354D).
Related to Fig. 3. a, Single-particle pipeline yields the final cryo-EM reconstruction with the corresponding angular distribution and local resolution map. The local resolution map shows more flexibility and lower resolution in the 4-nt bulge that connects stem P2.1 and P13, and towards the end of stem P6 and P9.2. b, FSC curve shows 3.1 Å resolution according to the 0.143 cutoff. c, Cryo-EM B factor.
Extended Data Fig. 8 Comparisons of apo L-21 and holo L-16 ScaI ribozyme cryo-EM models with previous crystal structures show structural conservation and metal ion shifts in the guanosine binding site among group I introns.
Related to Fig. 4. a–c, The apo L-21 ScaI ribozyme adopts a preorganized guanosine binding site (grey) that superimposes with previous crystal structures of mutated P3–P9 of the Tetrahymena ribozyme (a; green, PDB 1X8W), the Azoarcus ribozyme (b; violet, PDB 1U6B), and the phage Twort ribozyme (c; yellow, PDB 1y0q). d–g, The holo L-16 ScaI ribozyme (sky blue) superimposes with apo L-21 ScaI ribozyme (d; grey), the Azoarcus ribozyme (e; violet), the phage Twort ribozyme (f; yellow), and mutated P3–P9 of the Tetrahymena ribozyme (g; green). MC is absent in the apo L-21 ScaI ribozyme, whereas MC in the Azoarcus ribozyme is shifted compared to the holo L-16 ScaI ribozyme. Dash line indicates metal ion coordination with surrounding atoms.
Extended Data Fig. 9 Metal ion validations by distance and Q-score analysis, and illustrations of the apo L-21 and holo L-16 ScaI ribozyme cryo-EM structures compared with previous crystal structures.
a, Distances between metal ions and other atoms in the apo L-21 ScaI ribozyme model. b, Distances between metal ions and other atoms in the holo L-16 ScaI ribozyme model. c, Q-score analysis per metal ion of the apo L-21 and holo L-16 ScaI ribozyme cryo-EM models and maps. d, Metal core region of the holo L-16 ScaI ribozyme, visualized at 1.1σ threshold. e, Comparisons of the apo L-21 (grey) and holo L-16 (sky blue) ScaI ribozyme cryo-EM models with P4–P6 Delta C209 (blue, PDB 1HR2) and mutated P3–P9 of the Tetrahymena ribozyme (green, PDB 1X8W) in the same view as d. f, Catalytic site of the holo L-16 ScaI ribozyme, visualized at 1.4σ threshold. g, Comparisons of the apo L-21 (grey) and holo L-16 (sky blue) ScaI ribozyme cryo-EM models with the Azoarcus ribozyme (violet, PDB 1U6B), mutated P3–P9 of the Tetrahymena ribozyme (green, PDB 1X8W), and the phage Twort ribozyme (yellow, PDB 1Y0Q) in the same view as f. See also Supplementary Table 2.
This file contains Supplementary Tables 1-2.
Cryo-EM map and model of the apo L-21 ScaI Tetrahymena ribozyme with zoom in views of newly discovered tertiary interactions and representative metal ions shown in Figure 2, accompanied with the updated secondary structure.
Comparison of the apo L-21 and holo L-16 Tetrahymena ribozyme cryo-EM maps and models reveals substantial conformational change upon substrate binding.
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Su, Z., Zhang, K., Kappel, K. et al. Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature 596, 603–607 (2021). https://doi.org/10.1038/s41586-021-03803-w
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