7XSM

Misfolded Tetrahymena ribozyme conformation 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM.

Li, S.Palo, M.Z.Pintilie, G.Zhang, X.Su, Z.Kappel, K.Chiu, W.Zhang, K.Das, R.

(2022) Proc Natl Acad Sci U S A 119: e2209146119-e2209146119

  • DOI: https://doi.org/10.1073/pnas.2209146119
  • Primary Citation of Related Structures:  
    7XSK, 7XSL, 7XSM, 7XSN

  • PubMed Abstract: 

    The Tetrahymena group I intron has been a key system in the understanding of RNA folding and misfolding. The molecule folds into a long-lived misfolded intermediate (M) in vitro , which has been known to form extensive native-like secondary and tertiary structures but is separated by an unknown kinetic barrier from the native state (N). Here, we used cryogenic electron microscopy (cryo-EM) to resolve misfolded structures of the Tetrahymena L-21 ScaI ribozyme. Maps of three M substates (M1, M2, M3) and one N state were achieved from a single specimen with overall resolutions of 3.5 Å, 3.8 Å, 4.0 Å, and 3.0 Å, respectively. Comparisons of the structures reveal that all the M substates are highly similar to N, except for rotation of a core helix P7 that harbors the ribozyme's guanosine binding site and the crossing of the strands J7/3 and J8/7 that connect P7 to the other elements in the ribozyme core. This topological difference between the M substates and N state explains the failure of 5'-splice site substrate docking in M, supports a topological isomer model for the slow refolding of M to N due to a trapped strand crossing, and suggests pathways for M-to-N refolding.


  • Organizational Affiliation

    MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (388-MER)A [auth N]388Tetrahymena thermophila
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122579
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21 AI145647

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection