Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing

Luo, Bingnan; Zhang, Chong; Ling, Xiaobin; Mukherjee, Sunandan; Jia, Guowen; Xie, Jiahao; Jia, Xinyu; Liu, Liu; Baulin, Eugene F.; Luo, Yongbo; Jiang, Longxing; Dong, Haohao; Wei, Xiawei; Bujnicki, Janusz M.; Su, Zhaoming

doi:10.1038/s41929-023-00934-3

Cited by 16 publications

(2 citation statements)

References 95 publications

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“…We also described several ion pair types and showed how they "assemble" to form ionic chains (Figure 15). The characterisation of intricate ion pairs might provide an understanding of the formation of such motifs in RNA, other biopolymers and their catalytic sites (74,(91)(92)(93)(94)(95). We also described binding patterns that could not be easily rationalized, some of them being related to metal-mediated pairs possibly involving the participation of a transition metal present in the structure as a contaminant (Figure 14).…”

Section: Stereochemistry Is An Efficient Tool To Assign Mg 2+ Ionsmentioning

confidence: 97%

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺

Leonarski,

Henning-Knechtel,

Kirmizialtin

et al. 2024

Preprint

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The importance of Mg2+ions for RNA structure and function can difficultly be overstated. Several attempts were made to establish a comprehensive Mg2+binding site classification. However, such descriptions were hampered by poorly modelled ion binding sites. Recently, ribosome cryo-EM structures with resolutions < 2.0 Å allowed more detailed ion binding site descriptions. However, such a task is challenging. In a recent 1.55 Å E. coli ribosome structure (PDBid 8B0X), ion assignment incompleteness/errors were observed that prevent a full understanding of the chelated ion structures. We reinspected this cryo-EM reconstruction by using stereochemical constraints derived from an updated analysis of the Mg2+/K+occurrences in the Cambridge Structural Database (CSD) and established sufficiently straightforward and general binding principles to be applicable to any RNA of sufficient resolution. Through our improved characterization of the RNA ionic structure, we assigned all Mg2+ions bound to 2 to 4 non-water oxygens leading to a better understanding of the role of Mg2+ions in folding while shedding light on the importance of Mg2+...Mg2+/K+ion pairs in catalytic systems. Based on these data, we defined general Mg2+binding rules allowing to describe unanticipated motifs where up to five adjacent nucleotides wrap around a single ion.

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Section: Stereochemistry Is An Efficient Tool To Assign Mg 2+ Ionsmentioning

confidence: 97%

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺

Leonarski,

Henning-Knechtel,

Kirmizialtin

et al. 2024

Preprint

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“…By superimposing structures of homologous RNAs, it becomes possible to discern conserved and variable segments [3], which is commonly used in template-based RNA structure modeling [4]. The 3D superposition of distinct structures of RNA molecules proves beneficial in studies of functionally-related dynamics, such as those between different stages of self-splicing of introns [5] or between apo- and holo- states of riboswitches [6]. Furthermore, RNA 3D structure superposition is invaluable for inferring correct sequence alignments [7], given that RNA exhibits significantly less conservation at the sequence level compared to its structural conservation [8].…”

Section: Introductionmentioning

confidence: 99%

ARTEMIS - a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

Bohdan,

Bujnicki,

Baulin

2024

Preprint

Self Cite

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Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.

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Challenges, advances, and opportunities in RNA structural biology by Cryo-EM

Bonilla,

Jang

2024

Current Opinion in Structural Biology

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Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing

Cited by 16 publications

References 95 publications

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺

ARTEMIS - a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

Challenges, advances, and opportunities in RNA structural biology by Cryo-EM

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Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing

Cited by 16 publications

References 95 publications

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg2+

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg2+

ARTEMIS - a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

Challenges, advances, and opportunities in RNA structural biology by Cryo-EM

Contact Info

Product

Resources

About

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺

Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg²⁺