[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleSelf-splicing and cyclization mechanisms of the full-length Anabaena pre-tRNA.
Journal, issue, pagesNat Chem Biol, Vol. 22, Issue 6, Page 948-959, Year 2026
Publish dateApr 14, 2026
AuthorsXiaojing Zhang / Linfeng An / Wen Yang / Ran Yi / Ji Liu / Shanshan Li / Kaiming Zhang /
PubMed AbstractGroup I introns are catalytic RNAs capable of self-splicing and generating circular RNAs, processes central to RNA metabolism and biotechnology. Yet, full-length ribozyme structures containing entire ...Group I introns are catalytic RNAs capable of self-splicing and generating circular RNAs, processes central to RNA metabolism and biotechnology. Yet, full-length ribozyme structures containing entire exon sequences and the structural basis of postsplicing circularization have remained limited. Using cryo-electron microscopy, we resolved multiple conformational states of the full-length Anabaena tRNA(Leu) precursor, capturing key intermediates of splicing and cyclization. In the apo state, the exons preassemble into a mature tRNA-like conformation that promotes P1 helix formation. Transitions through the splicing states involve substantial rearrangements essential for catalysis. Unlike other group I introns, the Anabaena intron circularizes without sequence loss, using its guanosine-binding site as the catalytic center. Mutational analyses confirm that G37 reorientation and a conserved wobble receptor motif precisely position the circularization site, driving efficient cyclization even in engineered PIE systems. These findings uncover unique mechanisms of RNA catalysis and establish structure-based optimization for advancing RNA circularization technologies.
External linksNat Chem Biol / PubMed:41981295
MethodsEM (single particle)
Resolution3.38 - 5.28 Å
Structure data

62189

9k9g

EMDB-62189, PDB-9k9g:
Cryo-EM structure of Anabaena tRNA(Leu) precursor at Apo state
Method: EM (single particle) / Resolution: 3.38 Å

62190

9k9h

EMDB-62190, PDB-9k9h:
Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-1S state
Method: EM (single particle) / Resolution: 3.56 Å

62191

9k9j

EMDB-62191, PDB-9k9j:
Cryo-EM structure of linear intron of Anabaena tRNA(Leu) precursor
Method: EM (single particle) / Resolution: 3.46 Å

62192

9k9k

EMDB-62192, PDB-9k9k:
Cryo-EM structure of circular intron of Anabaena tRNA(Leu) precursor
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-65891: Cryo-EM structure of Anabaena tRNA(Leu) precursor at Pre-2S state
Method: EM (single particle) / Resolution: 5.28 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-GMP:
GUANOSINE

Source
  • anabaena (bacteria)
KeywordsRNA / Anabaena tRNA(Leu) precursor / Self-folding / Splicing / Cyclization / Cryo-EM

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more