6GYV

Lariat-capping ribozyme (circular permutation form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50004 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 

wwPDB Validation

Currently 6GYV does not have a wwPDB validation report.


This is version 1.0 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: 10.1073/pnas.1322248111
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Architecture et Réactivité de l'ARN, Unité Propre de Recherche 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Centre National de la Recherche Scientifique, 67084 Strasbourg, France;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Lariat-capping ribozymeA192Didymium iridis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50004 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.630α = 90.00
b = 85.710β = 90.00
c = 108.530γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXphasing

Structure Validation

Currently 6GYV does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release