4P8Z

Speciation of a group I intron into a lariat capping ribozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

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This is version 1.3 of the entry. See complete history


Literature

Speciation of a group I intron into a lariat capping ribozyme.

Meyer, M.Nielsen, H.Olieric, V.Roblin, P.Johansen, S.D.Westhof, E.Masquida, B.

(2014) Proc Natl Acad Sci U S A 111: 7659-7664

  • DOI: https://doi.org/10.1073/pnas.1322248111
  • Primary Citation of Related Structures:  
    4P8Z, 4P9R, 6GYV

  • PubMed Abstract: 

    The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core. The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching.


  • Organizational Affiliation

    Swiss Light Source at Paul Scherrer Institute, 5232 Villigen, Switzerland;


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Didymium iridis partial IGS, 18S rRNA gene, I-DirI gene and partial ITS1188Didymium iridis
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.56α = 90
b = 88.86β = 90
c = 105.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-BLAN-1502-02

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-10-04
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description