4R0D image
Entry Detail
PDB ID:
4R0D
Keywords:
Title:
Crystal structure of a eukaryotic group II intron lariat
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-07-30
Release Date:
2014-10-01
Method Details:
Experimental Method:
Resolution:
3.68 Å
R-Value Free:
0.27
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:GROUP IIB INTRON LARIAT
Chain IDs:A
Chain Length:622
Number of Molecules:1
Biological Source:Pylaiella littoralis
Polymer Type:polyribonucleotide
Description:LIGATED EXONS
Chain IDs:B
Chain Length:20
Number of Molecules:1
Biological Source:Pylaiella littoralis
Primary Citation
Crystal structure of a eukaryotic group II intron lariat.
Nature 514 193 197 (2014)
PMID: 25252982 DOI: 10.1038/nature13790

Abstact

The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 Å. This revealed that two tandem tetraloop-receptor interactions, η-η' and π-π', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.

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