5J01

Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a group II intron lariat primed for reverse splicing.

Costa, M.Walbott, H.Monachello, D.Westhof, E.Michel, F.

(2016) Science 354: --

  • DOI: 10.1126/science.aaf9258
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in b ...

    The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in branched ("lariat") form show that the 2'-5' branch organizes a network of active-site tertiary interactions that position the intron terminal 3'-hydroxyl group into a configuration poised to initiate reverse splicing, the first step in retrotransposition. Moreover, the branchpoint and flanking helices must undergo a base-pairing switch after branch formation. A group II-based model of the active site of the nuclear splicing machinery (the spliceosome) is proposed. The crucial role of the lariat conformation in active-site assembly and catalysis explains its prevalence in modern splicing.


    Organizational Affiliation

    Group II introns as ribozymes and retrotransposons, Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, Commissariat √† l'Energie Atomique et aux Energies Alternatives (CEA), University Paris-Sud, University Paris-Saclay, 1 Avenue de la Terrasse, B√Ętiment 26, 91198 Gif-sur-Yvette cedex, France. maria.costa@i2bc.paris-saclay.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
group II intron lariatA418Oceanobacillus iheyensis
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.930α = 90.00
b = 262.580β = 90.00
c = 69.040γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Derived calculations