9V7O | pdb_00009v7o

Cryo-EM structures of the Azoarcus pre-tRNA(ILE) conformation b undergoing the first-step self-splicing


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Pre-splicing conformation and stepwise circularization of a group I intron in Azoarcus pre-tRNA.

Hong, Y.Liu, J.Zhang, X.Liu, J.Li, S.Zhang, K.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70747-y
  • Primary Citation Related Structures: 
    9V7N, 9V7O, 9V7P, 9V7Q, 9X6B

  • PubMed Abstract: 

    Group I introns are catalytic RNAs capable of self-splicing, yet structural insights into full-length precursor RNAs and post-splicing circularization have been limited. Here, we present cryo-EM structures of the Azoarcus pre-tRNA Ile system across key catalytic stages, including the full-length precursor in Pre-1S conformations, the linear intron, and the circular introns, at 2.8-3.3 Å resolution. These structures reveal a preformed P1 helix, register shifts during splicing, and a conformational flip of G37 that stabilizes the circularization site. Biochemical analyses confirm a two-step circularization mechanism, generating a secondary circular product via an alternative ligation site. Together, our results provide an atomic-level view of a group I intron system through splicing and circularization. This work uncovers structural principles governing RNA conformational dynamics, catalysis, and circular RNA formation, with broad implications for ribozyme engineering.


  • Organizational Affiliation
    • Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, The RNA Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 276.01 kDa 
  • Atom Count: 6,109 
  • Modeled Residue Count: 284 
  • Deposited Residue Count: 852 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (284-MER)A [auth B],
B [auth D],
C [auth E]
284Azoarcus olearius
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.7

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-27
    Changes: Data collection, Database references