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TitleSnapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 1294, Year 2023
Publish dateMar 16, 2023
AuthorsShanshan Li / Michael Z Palo / Xiaojing Zhang / Grigore Pintilie / Kaiming Zhang /
PubMed AbstractGroup I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self- ...Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5'-splice site analog product and a 3'-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2'-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing.
External linksNat Commun / PubMed:36928031 / PubMed Central
MethodsEM (single particle)
Resolution2.35 - 3.41 Å
Structure data

33811

7yg8

EMDB-33811, PDB-7yg8:
Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 2.97 Å

33812

7yg9

EMDB-33812, PDB-7yg9:
Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 2.68 Å

33813

7yga

EMDB-33813, PDB-7yga:
Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 2.35 Å

33814

7ygb

EMDB-33814, PDB-7ygb:
Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 2.62 Å

33815

7ygc

EMDB-33815, PDB-7ygc:
Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 2.65 Å

33816

7ygd

EMDB-33816, PDB-7ygd:
Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing
Method: EM (single particle) / Resolution: 3.41 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • tetrahymena (eukaryote)
  • tetrahymena thermophila (eukaryote)
KeywordsRNA / Tetrahymena ribozyme / second step of self-splicing / conformation 5 / conformation 1 / conformation 2 / conformation 3 / conformation 4

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